Are you forgetting the part where Derek got tazed and was taken some where? Cameron had to go rescue him remember??
I don't think those people at the desert factory are/were Weaver's people to begin with. I believe there are 2 factions involved. Why would Weaver go massacre her employees after hearing the transmission that John Henry picked up? All that message said was "someone got shot. We have to relocate." or something like that. If she wanted to cover her tracks, she'd help them move. Why would she risk losing all the work that was done there?
There were no switch of employers IMO. The people at the desert factory, the men that attacked the light house, the men that captured Derek and tried to kill Cameron and the ones who captured Sarah are working for John Henry's "brother".