There is insufficient basis for making such a comparison. It's highly questionable that an ethical system can be "right" in the same way that a physical theory can be "right". There is an obvious standard by which to evaluate the rightness of a scientific theory: just check whether its factual claims accurately describe reality. The "system-is" must match the "reality-is" But a moral system is made out of oughts, not descriptive statements. The "system-ought" should be matching... exactly what? We don't even know, or aren't able to talk about, our "reality-oughts" without reference to either our intuitions or our moral system. If the latter, any moral system is self-referential and thus with no necessary grounding in reality, and if the former, then our foundational morality is our system of moral intuitions, and an ethical system like utilitarianism necessarily describes it or formalises it and may be superfluous. And the entire thesis of your post is that "reality-oughts" may turn out to fly in the face of our intuitions. This undermines the only basis there is for solving the is-ought problem.
The reason you expect some morally unintuitive prescriptions to prevail seems to rely on choosing the systemically-consistent way out of extreme moral dilemmas, however repugnant it may be. Now (I should mention I'm a total pleb in physics, please contradict me if this is wrong) we generally know reality to be self-consistent by necessity, and we aspire towards building self-consistent physical models of the world, at the expense of intuitions. Doing otherwise is (?) including magic as a feature in our model of the world. In the moral realm, to accept inconsistency would be to accept hypocrisy as a necessity, which is emotionally unpalatable just like physical-system inconsistency is confusing. But it is not obvious that morality is ultimately self-consistent rather than tragic. Personally I incline towards the tragedy hypothesis. Bending over backwards for self-consistency seems to be a mistake, as evidenced by repugnant conclusions of one sort or another. The fact that your moral system pits consistency values against object-level values in extreme ethical dilemmas seems to be a strike against it rather than against those object-level values.
About utilitarianism specifically: if you have your zeitgeist-detection-goggles on, it's easy to see utilitarianism as a product of its contemporary biases: influenced by a highly economical worldview. Utility can be described as moral currency in some aspects. It does even worse in introducing glitches and absurdities than its economical counterpart, because it's a totalising ethical notion -- one which aims to touch every aspect of human existence, instead of being confined to the economic realm. Utility is a quantitative approach to value that attempts to collapse qualitatively different values into one common currency of how much satisfaction can be extracted from any of them. My go-to example for this is Yudkowsky's torture vs. dust specks, which fails to distinguish between bad and evil (nuances are, apparently, for unenlightened pre-moderns), upping the amount of badness to arbitrary levels until it supposedly surpasses evil. This kind of mindset is, at its most charitable understanding, a useful framework for a policy-maker that has to direct finite resources to alleviating either a common and slight health problem (say, common colds or allergies) or a rare and deadly disease. Again, a problem that is economic in nature, that has a dollar value. Utilitarianism is also popular around here for being more amenable to computational (AI) applications than other ethical systems. Beyond that, to hail it as the ultimate moral system is excessive and unwarranted.
Utilitarianism sometimes supports weird things: killing lone backpackers for their organs, sacrificing all world's happiness to one utility monster, creating zillions of humans living on near-subsistence level to maximize total utility, or killing all but a bunch of them to maximize average utility. Also, it supports gay rights, and has been supporting them since 1785, when saying that there's nothing wrong in having gay sex was pretty much in the same category as saying that there's nothing wrong in killing backpackers. This makes one wonder: if despite all the disgust towards them few centuries ago, gay rights have been inside the humanity's coherent extrapolated volition all along, then perhaps our descendants will eventually come to the conclusion that killing the backpacker has been the right choice all along, and only those bullet-biting extremists of our time were getting it right. As a matter of fact, as a friend of mine pointed out, you don't even need to fast forward few centuries - there are or were already ethical systems actually in use in some cultures (e.g. bushido in pre-Meiji restoration Japan) that are obsessed with honor and survivor's guilt. They would approve of killing the backpacker or letting them kill themselves - this being an honorable death, and living while letting five other people to die being dishonorable - on non-utilitarian grounds, and actually alieve that this is the right choice. Perhaps they were right all along, and the Western civilization bulldozed through them effectively destroying such culture not because of superior (non-utilitarian) ethics but for any other reason things happened in history. In this case there's no need in trying to fix utilitarianism, lest it suggest killing backpackers, because it's not broken - we are - and out descendants will figure that out. In physics we've seen this, when an elegant low-Kolmogorov-complexity model predicted that weird things happens on a subatomic level, and we've built huge particle accelerators just to confirm - yep, that's exactly what happens, in spite of all your intuitions. Perhaps smashing utilitarianism with high energy problems only breaks our intuitions, while utilitarianism is just fine.
But let's talk about relativity. In 1916 Karl Schwarzschild solved the newly discovered Einstein field equations and thus predicted the black holes. It was thought as a mere curiosity and perhaps GIGO at the time, until in 1960s people realized that yes, contra all intuitions, this is in fact a thing. But here's the thing: they were actually first predicted by John Michell in 1783. You can easily check it: if you substitute the speed of light to the classical formula for escape velocity, you'll get the Schwarzschild radius. Michell actually knew the radius and mass of the Sun, as well as the gravitational constant precisely enough to get the order of magnitude and the first digit right when providing an example of such object. If we somehow never discovered general relativity, but managed to build good enough telescopes to observe the stars orbiting the emptiness that we now call Sagittarius A*, if would be very tempting to say: "See? We predicted this centuries ago, and however crazy it seemed, we now know it's true. That's what happens when you stick to the robust theories, shut up, and calculate - you stay centuries ahead of the curve."
We now know that Newtonian mechanics aren't true, although they're close to truth when you plug in non-astronomical numbers (and even some astronomical). A star 500 times size and the same density as the Sun, however, is very much astronomical. It is only sheer coincidence that in this exact formula relativistic terms work exactly in the way to give the same solution for the escape velocity as the classical mechanics do. It would be enough for Michell to imagine that his dark star rotates - a thing that Newtonian mechanics say doesn't matter, although it does - to change the category of this prediction from "miraculously correct" to "expectedly incorrect". It doesn't mean that Newtonian mechanics weren't a breakthrough, better than any single theory existing at the time. But it does mean that it would be premature to people in pre-relativity era to invest into building a starship designed to go ten times the speed of light even if they could - although that's where "shut up and calculate" could lead them.
And that's where I think we are with utilitarianism. It's very good. It's more or less reliably better than anything else. And it managed to make ethical predictions so far fetched (funny enough, about as far fetched as the prediction of dark stars) that it's tempting to conclude that the only reason why it keeps making crazy predictions is that we haven't yet realized they're not crazy. But we live in the world where Sagittarius A* was discovered, and general relativity wasn't. The actual 42-ish ethical system will probably converge to utilitarianism when you plug in non-extreme numbers (small numbers of people, non-permanent risks and gains, non-taboo topics). But just because it converged to utilitarianism on one taboo (at the time) topic, and made utilitarianism stay centuries ahead of the moral curve, doesn't mean it will do the same for others.