Seriously ambiguous pronouns

The intro to Terminator: The Sarah Conner Chronicles goes something like:

In the future, my son will lead humanity in the war against Skynet, a computer system programmed to destroy the world. It has sent machines back through time, some to kill him, one to protect him.

The only reading I get on this is that "it" refers to Skynet, and thus Skynet has sent machines back to kill John Conner as well as protect him. So I'm only a few episodes into Season I on Netflix Instant, so perhaps I'm about to find out that Skynet is playing some weird kind of Robert Jordan game, but I suspect rather the writers wanted "it" to refer to "the war". I can get that reading if I squint, but it seems incredibly unnatural.