So, a lot of people's first introduction to all of this was the comment Sam made in his article "What I've Learned From Female Founders So Far" about how "we're working on something to improve the quality of Hacker News comments". It is thereby not surprising that people are trying to analyze whether this feature will help that specific issue ;P.
FWIW, I think that this is a different problem than the "you are an idiot" problem: I think a lot of the threads that people are finding issue with when it comes to attitudes towards under-represented groups are not (at least entirely) filled with this "explicit type" of negative comment: it is instead the more insidious, implicit type being stared at.
Regardless, I don't see why the endorsement system will somehow work against either of these problems when the voting mechanism hasn't: the comments that start with "you are an idiot, don't you realize that" are currently getting upvotes, so why would we presume they won't also get endorsements? Are high-karma users voting differently?