You just answered your own question. It's better to end something rather than let that possibility come around, and Rorschach didn't want to be a part of a world that didn't know the truth.
Hmm...that sounds fair enough, from Dr. Manhattan's viewpoint at least. Did he even know that Rorschach didn't have his journal on him, especially with the tachyons disrupting his precognition (funny how he describes time as being simultaneous for him, yet throw in a couple of tachyons and it blocks the future for him - or maybe he was lying)? Then again, did he even know that Rorschach had a journal in the first place, and that he was writing down all the events of his investigation in it?
But yeah, perhaps that just doesn't matter and he didn't want to take the risk. I've always found the "thermodynamic miracle" excuse odd, though. I've made another thread concerning Dr. Manhattan, so we can discuss that there, but I don't know whether or not a woman falling in love with a man who almost raped her and bearing his child is really that big a deal, unless that wasn't Alan Moore's point.