I don't think it was Weaver's men that kidnapped Sarah. The bald guy who kidnapped Sarah worked at the factory in the desert and Weaver blew it up. I believe that the guys that captured Derek, the guys that attacked the light house, and the terminator that attacked the Weaver resident were John Henry's "brother"'s men. It tried to hack John Henry but failed so it retaliated. That's why the men had a picture of Savannah on their phones. It was there next target. A terminator was sent to do the job because humans are taken out easily.
Like others have said, I think Weaver is on the "good" side. I don't see the contradicting evidence at all. Sure she was ruthless but her actions were to stop the evil Skynet.