There's also the fact that Judgment Day (the new,new,new one ) is in 2007 according to Cameron. If Sarah had already helped Judgement Day happen in 1999, the Terminator would have no problem with killing her. If she did after 1999, Skynet would already be gone - i.e. they skipped 2000 - 2006, so Sara couldn't have done anything then. She originally died on December 4, 2005 from Cancer, so it's not like she would have done anything in 2007 to create Skynet.
This whole Judgement Day does get a little convoluted to say the least.
I guess my theory applies to future writing not yet done. Maybe the T's could have killed Sarah before this last jump -- but now with everything in 2007, maybe they actually need her now. Maybe she's the one who "pushes the red button" sort of thing.
I'm sure if the show goes the distance, this idea -- this inevitable threat to everything Sarah is fighting against -- will come to the writers. It's a great tragic future for Sarah to come to realize: that she initiates Judgement Day...and there's nothing she can do to change that. Although she will no doubt spend many episodes trying.
The inevitability of the event, and her struggle against it -- much like John's struggle against becoming the supreme leader -- is great drama!