I feel a strong affinity with this community, but that's hard to remember when my own locally-weird ideas get downvoted and/or reverted to draft without giving me a clear route to explain myself.
Even just splitting the Karma mechanism into "doesn't seem benevolent" and "doesn't seem accurate" would be much more comforting. None of us have the working memory to keep that straight all the time.
Or, since nonbenevolence is a stronger claim, it could be the Strong Downvote? It should absolutely be labeled as such, though.
I think there is a value to downvoting being easy, and not require an explanation (Eliezer talked about that being important from the start), but I do agree with you that it can be frustrating.
So, I suggest a better solution would look in the opposite direction, of rewarding articulate downvoting. How exactly I'm not sure, but I think it would be better than something that discourages downvoting.
I guess there's already some of that, since if you explain your down vote in a comment then it can get upvoted. But it can also be ignored or downvoted, so it's not a reliable reward.
One way to elicit more articulate downvoting is to explicitly request constructive criticism at the end of a post.