Removing comments happens silently and without a trace. Such tools can be used by the establishment to quiet dissent.

So let's have a policy that banned commenters get to post a link to their anti-LW blog. We could list all the anti-LW blogs on a wiki page or something.

They can break existing conversations.

By removing examples of what not to do, we can no longer point at them as examples.

I don't think anyone is proposing to delete past comments.

We need more contrarians, not fewer.

If I promise to be a high-quality contrarian, can we ban the next five low-quality contrarians?

discourage participation amongst those who are in particular need of our help

This is a good thing. LW's positive impact is likely to lie mostly in building an effective movement, figuring out what issues are important, and pushing on those issues; all of these are helped by a high average level of rationality. LW's positive impact is unlikely to lie in trying to fix whatever hopeless cases wander by.

Freedom of speech is valuable in itself, and its presence here is aesthetically pleasing.

I disagree on both counts, and I suspect your other arguments may be rationalizations springing from this value judgement.