Hmm... Since Cloud does know of Mother, at least a bit, maybe Jenova wasn't destroyed just then. It might be that he was mid-way through the process that was supposed to turn him into a Sephiroth clone, and something happened to her then... Zack managed to get out for a short while? Maybe, while escaping, Zack decided to take care of that bitch in the reactor that drove his friend(s) insane?
Also, "Franken-swiss cheese" as a description of Cloud's mind? Absolutely priceless. I love it. *grin*