The Batman-themed books (which I'd say Batgirl is part of) mostly kept the previous continuity intact, I mean they didn't have to keep "The Killing Joke" in at all and just had Barbara Gordon be Batgirl and forget about the whole paralysis/Oracle thing. But Barbara shows a bit of apprehension in her battles and something about what happened to her is holding her back (and I doubt it's all in "survivor's guilt.") I suspect some sort of sexual assault occurred between her and this other guy (again, that one took place is pretty heavily suggested in The Killing Joke, as The Joker shows Gordon nude photos of Barbara during his captivity.) Maybe not full on rape with penetration (which may not have been possible given her injuries) but some-kind-of assault seemed to have taken place.
I doubt the other guy is The Joker since that would a)ruin The Joker's motivations in "The Killing Joke" and b)this guy doesn't have the characteristic facial structure of The Joker.
I guess we'll see next month.