I don't necessarily see how Bats reaction was such a bad thing. I'm pretty sure that's a theme TDK will play heavily on, too.
Fact is, Joker is a force of nature that Bruce didn't expect at all, so it's understood why he'd be so confused during their first few meet-ups.
As for the origin, I honestly didn't mind it. Yes, Joker's history has always been referred to as ambiguous. But for a character who we're not supposed to know before the clown facade, he's had quite a few origins ironically enough.
I always preferred a pre-Joker who was always a little screwed up in the head. Never made sense to me for one terrible accident to completely do a 180 on a person's psyche. Adding in the hitman element and compulsion for daredevil acts, helped develop the character and explain his trademark behavior.