Hunters are a challenge, no doubt - and if that Hunter out-gears you then I don't think there's any shame in losing out by 5%
Gearing up and ensuring said gear is absolutely top-notch is one option (I'm guessing that you have to rotations down and obviously know your class) but I raid with a BM hunter and even in equal gear I can never guarantee I'll beat them - there's not much in it either way but BM DPS is quite frankly, insane as long as he can use his pet.
I don't think that the generalisation that Affliction Warlock DPS in Karazhan is inaccurate - If anything little problems like this aren't by any means common so its more indicative of that particular Hunter outgearing you - you can and will catch up.