Down votes aren't disagreement votes. If you have an issue with their comment then reply, but don't put them into the negative because you don't like the facts they point out.
You're explicitly wrong about downvoting being a mark of disagreement. That's been black-letter HN culture since forever. I don't entirely like it either (though I'll admit that I do it, too), but 'pg repeatedly went on record, saying he meant for it to be that way.
That said, I can't stand it when people downvote comments pointing out objective, verifiable facts that they don't like. It happens all the time, and I despair a bit for the quality of discourse even possible in a community where that's a thing that people do.
