You are presenting an oversimplified picture in both cases, and the contrast is definitely not so clear-cut.
First, the christological and other theological controversies were often only part of much broader political, ideological, ethnic, and other conflicts, involving all sorts of parties and factions both within and outside the church hierarchy. Sometimes there was also a strong populist element -- during the monophysite controversy, for example, there were plenty of spontaneous riots and pogroms. Therefore, in these controversies, the power and status of many groups and individuals was at stake, not just the interests of the Church leadership.
Second, the modern repercussions of various ideological transgressions are by no means limited to spontaneous reactions by people who feel directly targeted. For start, there is a complicated and non-obvious system that determines which groups are entitled to such reaction, so that their outrage will be supported and the offenders condemned by the respectable opinion, and which groups are OK to denigrate, so that protesting will only lower their status still further. Then, we also have a network of official intellectual institutions that have a de facto monopoly of respectable and impactful thinking, and the reaction of these institutions to various ideological transgressions involves many elements far beyond direct and spontaneous outrage of those who are (supposed to be) directly targeted.
But aside from all this, my main point is the contrast between two kinds of systems that is independent of the issues you raise:
A system in which certain beliefs are clearly spelled out as official dogma that it is forbidden to question, so if you're accused of heresy, you can at least demand a clear statement of what exact official dogma you have contradicted -- and if you have in fact steered clear of any matters of official dogma in your writings and utterances, this is admissible as a valid defense. (Historically, this was typically the case for people accused of heresy by the Church tribunals, though of course things varied a lot in different places and times and there were certainly instances of corruption and railroading, like in any other legal system.)
A system in which there is official pretense that there is no dogma whatsoever, that everyone is supposed to be a skeptical free thinker about everything, and that imposing some sort of official dogma would be the vilest tyranny imaginable -- so that when you are accused of some ideological transgression, it is automatically assumed that your statements must be due to either disingenuous malice or some crazy delusion, since the respectable opinion is considered to be a product of pure rational thinking, as an assumption built into the system. So rather than having clearly outlined boundaries of what you may or may not say, you must pretend to be a free thinker unencumbered by any official dogma, while at the same time strictly adhering to the de facto official dogma -- which is only more sweeping and onerous because it is so vague and not stated openly.
It seems to me that system (2) is hardly an improvement over (1).
Years ago, my first girlfriend (let's call her 'Alice') ran into her ex-boyfriend at a coffee shop. They traded anecdotes, felt connected, a spark of intimacy...
And then she left the coffee shop, quickly.
Later she explained: "You have my heart now, Luke."
I felt proud, but even Luke2005 also felt a twinge of "the universe is suboptimal," because Alice hadn't been able to engage that connection any further. The cultural scripts defining our relationship said that only one man owned her heart. But surely that wasn't optimal for producing utilons?
This is an account of some lessons in rationality that I learned during my journeys in romance.* I haven't been very rational in my relationships until recently, but in retrospect I learned a fair bit about rationality from the failures resulting from my irrationality in past relationships.
Early lessons included realizations like the one above — that I wasn't happy with the standard cultural scripts. I hadn't really noticed the cultural scripts up until that point. I was a victim of cached thoughts and a cached self.
Rationality Lesson: Until you explicitly notice the cached rules for what you're doing, you won't start thinking of them as something to be optimized. Ask yourself: Which parts of romance do you currently think of as subjects of optimization? What else should you be optimizing?
Gather data
At the time, I didn't know how to optimize. I decided I needed data. How did relationships work? How did women work? How did attraction work? The value of information was high, so I decided to become a social psychology nerd. I began to spend less time with Alice so I could spend more time studying.
This wasn't easy. She and I had connected in some pretty intimate ways, including a simultaneous deconversion from fundamentalist Christianity. But in the end my studies paid off. Moreover, my studies in personality and relationship styles helped me to realize that I (and therefore she) would have been miserable if I had decided to pursue marriage with her (or anyone at the time). Now that is valuable information to have!
Rationality Lesson: Respond to the value of information. Once you notice you might be running in the wrong direction, don't keep going that way just because you've got momentum. Stop a moment, and invest some energy in the thoughts or information you've now realized is valuable because it might change your policies, i.e., figuring out which direction to go.
Sanity-check yourself
Before long, Alice was always pushing me to spend more time with her, and I was always pushing to spend more time studying psychology. By then I knew I couldn't give her what she wanted: marriage.
So I broke up with Alice over a long conversation that included an hour-long primer on evolutionary psychology in which I explained how natural selection had built me to be attracted to certain features that she lacked. I thought she would appreciate this because she had previously expressed admiration for detailed honesty. Now I realize that there's hardly a more damaging way to break up with someone. She asked that I kindly never speak to her again, and I can't blame her.
This gives you some idea of just how incompetent I was, at the time. I had some idea of how incompetent I was, but not enough of one to avoid badly wounding somebody I loved.
Rationality Lesson: Know your fields of incompetence. If you suspect you may be incompetent, sanity-check yourself by asking others for advice, or by Googling. (E.g. "how to break up with your girlfriend nicely", or "how to not die on a motorcycle" or whatever.)
Study
During the next couple years, I spent no time in (what would have been) sub-par relationships, and instead invested that time optimizing for better relationships in the future. Which meant I was celibate.
Neither Intimate Relationships nor Handbook of Relationship Initiation existed at the time, but I still learned quite a bit from books like The Red Queen and The Moral Animal. I experienced a long series of 'Aha!' moments, like:
Within a few months, I had more dating-relevant head knowledge than any guy I knew.
Lesson: Use scholarship. Especially if you can do it efficiently, scholarship is a quick and cheap way to gain a certain class of experience points.
Just try it / just test yourself
Scholarship was warm and comfy, so I stayed in scholar mode for too long. I hit diminishing returns in what books could teach me. Every book on dating skills told me to go talk to women, but I thought I needed a completed decision tree first: What if she does this? What if she says that? I won't know what to do if I don't have a plan! I should read 10 more books, so I know how to handle every contingency.
The dating books told me I would think that, but I told myself I was unusually analytical, and could actually benefit from completing the decision tree in advance of actually talking to women.
The dating books told me I would think that, too, and that it was just a rationalization. Really, I was just nervous about the blows my ego would receive from newbie mistakes.
Rationality Lesson: Be especially suspicious of rationalizations for not obeying the empiricist rules "try it and see what happens" or "test yourself to see what happens" or "get some concrete experience on the ground". Think of the cost of time happening as a result of rationalizing. Consider the opportunities you are missing if you don't just realize you're wrong right now and change course. How many months or years will your life be less awesome as a result? How many opportunities will you miss while you're still (kinda) young?
Use science, and maybe drugs
The dating books told me to swallow my fear and talk to women. I couldn't swallow my fear, so I tried swallowing brandy instead. That worked.
So I went out and talked to women, mostly at coffee shops or on the street. I learned all kinds of interesting details I hadn't learned in the books about what makes an interaction fun for most women:
After a while, I could talk to women even without the brandy. And a little after that, I had my first one-night stand, which was great because it was exactly what she and I wanted.
But as time passed I was surprised by how much I didn't enjoy casual flings. I didn't feel engaged when I didn't know and didn't have much in common with the girl in my bed. I had gone in thinking all I wanted was sex, but it turned out that I wanted connection to another person. (And sex.)
Rationality Lesson: Use empiricism and do-it-yourself science. Just try things. No, seriously.
Self-modify to succeed
By this time my misgivings about the idea of "owning" another's sexuality had led me to adopt a polyamorous mindset for myself. (I saw many other people apparently happy with monogamy, but it wasn't for me.) But if I was going to be polyamorous, I needed to deprogram my sexual jealousy, which sounded daunting. Sexual jealousy was hard-wired into me by evolution, right?
It turned out to be easier than I had predicted. Tactics that helped me destroy my capacity for sexual jealousy include:
This lack of sexual jealousy came in handy when I later dated a polyamorous girl who was already dating two of my friends.
Rationality Lesson: Have a sense that more is possible. Know that you haven't yet reached the limits of self-modification. Try things. Let your map of what is possible be constrained by evidence, not by popular opinion.
Finale
There might have been a learning curve, but by golly, at the end of all that DIY science and rationality training and scholarship I'm much more romantically capable, I'm free to take up relationships when I want, I know fashion well enough to teach it at rationality camps, and I can build rapport with almost anyone. My hair looks good and I'm happy.
If you're a nerd-at-heart like me, I highly recommend becoming a nerd about romance, so long as you read the right nerd books and you know the nerd rule about being empirical. Rationality is for winning.
* My thanks to everyone who commented on earlier drafts of this post. Here are the biggest changes I made: