I mostly agree with the first 3/4 of your post. However...

Another problem is how you handle people who disagree with you and who you think are wrong. Concepts like "Well-Kept Gardens Die By Pacifism" will at some point explode in your face. I have chatted with a lot of people who left lesswrong and who portray lesswrong/SI negatively. And the number of those people is growing. Many won't even participate here because members are unwilling to talk to them in a charitable way. That kind of behavior causes them to group together against you. Well-kept gardens die by pacifism, others are poisoned by negative karma. A much better rule would be to keep your friends close and your enemies closer.

You can't make everyone happy. Whatever policy a website has, some people will leave. I have run away from a few websites that have "no censorship, except in extreme cases" policy, because the typical consequence of such policy is some users attacking other users (weighing the attack carefully to prevent moderator's action) and some users producing huge amounts of noise. And that just wastes my time.

People leaving LW should be considered on case-by-case basis. They are not all in the same category.

Why does that rational wiki entry about lesswrong exist?

To express opinions of rationalwiki authors about lesswrong, probably. And that opinion seems to be that "belief in many worlds + criticism of science = pseudoscience".

I agree with them that "nonstandard belief + criticism of science = high probability of pseudoscience". Except that: (1) among quantum physicists the belief in many worlds is not completely foreign; (2) the criticism of science seems rational to me, and to be fair, don't forget that scholarship is an officially recognized virtue at LW; (3) the criticism of naive Friendly AI approaches is correct, though I doubt the SI's ability to produce something better (so this part really may be crank), but the rest of LW again seems rational to me.

Now, how much rational are the arguments on the talk page of rational wiki? See: "the [HP:MoR link] is to a bunch of crap", "he explicitly wrote [HP:MoR] as propaganda and LessWrong readers are pretty much expected to have read it", "The stuff about 'luminosity' and self-help is definitely highly questionable", "they casually throw physics and chemistry out the window and talk about nanobots as if they can exist", "I have seen lots of examples of 'smart' writing, but have yet to encounter one of 'intelligent' writing", "bunch of scholastic idiots who think they matter somehow", "Esoteric discussions that are hard to understand without knowing a lot about math, decision theory, and most of all the exalted sequences", "Poor writing (in terms of clarity)", "[the word 'emergence'] is treated as disallowed vocabulary", "I wonder how many oracular-looking posts by EY that have become commonplaces were reactions to an AI researcher that had annoyed him that day" etc. To be fair, there are also some positive voices, such as: "Say what you like about the esoteric AI stuff, but that man knows his shit when it comes to cognitive biases and thinking", "I believe we have a wiki here about people who pursue ideas past the point of actual wrongness".

Seems to me like someone has a hammer (a wiki for criticizing pseudoscience) and suddenly everything unusual becomes a nail.

You are just lucky that they are the only people who really care about lesswrong/SI.

Frankly, most people don't care about lesswrong or SI or rational wiki.