This is the behavior we want to avoid.
It might help to ask why we want to avoid this. The most obvious reason is that the comments then become not visible to someone scanning the entire thread. If that's the concern, then that's a minor issue. Moreover, if that is the cause, then the situation will only become worse if people also can't see them in the recent comments thread.
Presumably, in the ideal universe, under most circumstances, people will start a new thread to discuss a relevant idea in a highly downvoted prior subthread. But a thread has turned into an actually productive entity, I don't see how that isn't a good thing.
What am I missing?
If the goal of collapsing downvoted comments is to make it easier for people to find valuable conversations without wasting their time reading downvoted comments, then having valuable conversations downstream of downvoted comments (such that, in order to read the valuable conversation, you also have to read the downvoted comment) subverts that goal.
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
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?"