You're right, of course, that hiding those comments doesn't guarantee that valuable conversations won't wind up downstream of them. But I'd expect it to lower the odds
Karma isn't synchronous, so the discussion can take place before the parent is downvoted. For example, this thread contains a discussion that probably mostly occurred before Eliezer's comment was voted down to -4... making this very thread an example of the reason why this shouldn't be done.
(Among other things, it means you can make an entire thread of conversation vanish by targeting a parent with a few downvotes, which really over-powers downvoters.)
A brief line from this comment indicates that the author of the cryonics-critical comment quoted here was perhaps not the one that deleted it.
Was it deleted by a moderator?
Honestly, the decisive downvoting seemed to do the trick of hiding it from casual readers who don't want to see the long annoying rants. I don't think it was casting any doubt on the credibility of cryonics.
While it sounds like the author regrets posting it, I would think they should be allowed to delete it themselves.
Edit: Originally titled "Cryonics critical comment deleted?"