Interesting. A couple hypotheses:
1) Admins overestimate the effect that certain policies have on behavior (they may underestimate random effects, or assign effects to the wrong policy); just like parents might overestimate the effect of parenting choices, or managers overestimate the impact of their decisions ("we did daily stand-up meetings, and the project was completed on time - the daily stand-up meetings must be the cause!").
2) Eliezer is more concerned about the public image of LessWrong (both because of how it reflects on CFAR and SIAI, and on the kind of people it may attract) than you are (were?) about the everything-list.
For what it's worth I'm fine with moderation of stupid things like discussing assassinations, and of banning obnoxious trolls and cranks and idiots, and the main reason to refrain from those kind of mod actions would be to avoid scaring naive young newcomers who might see it as an affront against Sacred Free Speech.
Your testimony of a case where you still have quality discussion with very light moderation makes me slightly less in favor of heavy-handed moderation.
(I'm not sure that the moderation here is becoming "stronger" recently, as opposed to merely a bit more explicit)
Eliezer has pretty blatantly stated that the reasoning was #2
http://wiki.lesswrong.com/wiki/Deletion_policy
This is my attempt to codify the informal rules I've been working by.
I'll leave this post up for a bit, but strongly suspect that it will have to be deleted not too long thereafter. I haven't been particularly encouraged to try responding to comments, either. Nonetheless, if there's something I missed, let me know.