As I understand the idea, endorsing a comment doesn't mean you agree with it. It just means you think it deserves to be in the thread. That should leave room for unpopular views as long as they're respectfully expressed.
Yeah, that's exactly how it will be used.
Sarcasm aside, the word "endorse" has a very specific definition which basically guarantees how this system will be used, intentions or not. I think about every single grayed-out comment I've seen, downvoted simply because it shared an opinion that made people feel uncomfortable but was nonetheless on-point, and now realize that we'll never even see those comments.
Real bummer for those inheriting HN to get it after this bad decision has been made. Will probably represent the end of useful dissent on HN.
That's why I think the notion of giving a really limited subset of reasons to upvote or downvote something could be potentially useful. "Inflammatory" or some other, much better word, would better describe why I downvoted something, and might make it easier to take appropriate action on that, or figure out if the post is a one off for the user, or typical of their habits.
All of this, of course, if heavily dependent on the moderators/creators of the community deciding what exactly they're trying to drive, as far as specific behavior (with or without the input of the community--it's their ship to guide).