I think Ron was able to get over his prejudice about werewolves when he had to reconcile the fact that it was Remus, but your point about his first reaction is spot on.

And it's only been a day for Ron, which is piled up with his thinking that Harry's trying to molest his little sister (which we all know is wrong, but ROn's got that protective jealous streak going on). Soon, it'll all, um, come to a head. (aka boom)