So I watched the movie for real (as opposed to just reading reviews and articles about the controversy) and I have to say that there's a cautionary tale there somewhere about not judging a work one hasn't actually consumed based on reports and rumors.
When I heard about the 'controversial' Batman/Batgirl scene, I too thought it may well ruin the film given that it seemed to be there just for shock value and as to pander to the few fans of a rather controversial 'ship'. The Internet exploded with reports about how Batgirl was objectified, how Batman was a dirty old man sleeping with someone who's a 'daughter' to him, how Bruce and Babs are breaking Dick's trust etc.
But having actually seen the scene in question, and that too in the context of the larger narrative of the first 30 or so minutes of the entire film...I have to say, that IF there could ever be a way to show Bruce and Barbara getting it on that WASN'T nausea-inducing on some level, then this film managed to accomplish it.
In a sense, I felt that sex scene wasn't anything to do with 'shipping' or 'romance' at all. Rather it had more to do with the nature of Batman and Batgirl's partnership, both personally and professionally - something which has been dealt with in various stories for years, and which has now been taken to one extreme conclusion. Batgirl looked up to Batman, was inspired by him, and wanted to do good in the world by emulating him. She got drawn into his orbit, emotionally. She wanted to be respected by him as an equal. But he refused to treat her as such. And then tension mounted and for a brief moment, Barbara's emotional and intellectual attraction to the Batman reached a flashpoint and became a sexual one (and perhaps the same can be said for Bruce). And 'it' happened.
And to the credit of both characters, neither of them were too happy about it. Bruce in particular. All the arguments we see online about Bruce taking advantage of Barbara...well, he didn't really take advantage of her but you can tell that Bruce certainly feels he might have done just that, which is why he tries to avoid Barbara and keep her at arm's length.
Granted, I do feel that the first half-hour or so ought to have perhaps belonged to another film, since it has very little to do with the actual 'Killing Joke' story beyond fleshing out the story's prime victim. Though I suppose there is a 'Psycho'-like feel to the structure - following a protagonist who, some time into the film, becomes the victim and we then switch to the 'real' (or rather next) protagonist.
The rest of the film is brilliant. The flashbacks were especially well done. The soundtrack does a great job building the atmosphere. There's a great film noir vibe throughout and a horror movie vibe once we get to the circus.
The ending in particular is a masterstroke. Batman randomly laughing to Joker's joke was something I never really 'got' with the original story but the adaptation really 'sold' that for me. In fact, that ominous last shot really made me remember Grant Morrison's theory about Batman killing the Joker...
On the whole, it was a great film. Maybe not THE best Batman animated film, but close enough (certainly more than a cut above the 'New 52' outings).