The thing to do would be to load a save from before the mission with Gibbed's editor, see which plot flags are set and correct accordingly.
Nah, there's no point in changing history, I've accept that the Geth died in my "canonical" playthrough. It actually made the decision to destroy the Reapers much easier since I didn't have the concern of killing off the Geth too. I just wanted to know why I wasn't given the option for peace. For two years I had assumed it was due to punching Admiral Han'Gerrel, but it seems now like it was down to a glitch.