And Weaver did go out there to squash it, didn't she? As for being worried, that was because she has just discovered a serious competitor in her own line of business (both regarding developping super AIs and collecting Coltan). I always thought this made way more sense than Weaver killing all of her own employees because someone made a mistake - I could understand killing those few directly responsible, but the whole plant? She was eliminating the competition. It does not help Skynet - Serrano point isn't "automated" in a vacuum, she is the one controlling it, ergo she is helping herself (and JH), not Skynet and not the Connors. Maybe Weaver just thinks it's handy to have control over important power sources (JH needs plenty of electical power, and Weaver does have her own Coltan factories, I suspect), and she could also anticipate some other version of Skynet trying to take control over it, which may give her an opportunity to identify this potential enemy when it makes a move at the plant when it's under her control/monitoring. It could also be an important point to use in negotiation with human resistance fighters like the Connors, if she ever has to treat with them (which I suspect is going to happen soon).