I've read most of the other stories online, which are good, by the way.
They could've done that, but then again, the whole idea is that judgement day is "going to happen anyways", it's inevitable, so the machines have don't have to worry about Skynet being built. I think they understand this better than any human ever did; until it was too late, of course. So what better way to stop the humans from succeeding than to hunt down Johns lieutenants?