I don't see it as a true "kidnapping", more of a very poor plan to "deprogram" a young girl who is very likely to be in a world of hurt if she continues to go along with the order.
Gemma? My theory has Gemma being shot or Gemma doing the shooting...
I only hear one gun shot. If it was a hand gun fired by The Order at Bree and/or Mr. Bree, wouldn't we expect to hear multiple rounds fired off? Plus the sound...I'm not a balistics expert, but the sound of the shot seems more ...