I was wondering this myself.
My only guess is that he went back and forth between personas while simultaneously keeping Ryuuko alive. Once his disloyalty was found out is when he faked his death and donned the Isshin persona full-time. Ryuuko does look older than her dumpster trash baby form during this episode's flashback, and it makes sense for Isshin to keep his Soichiro identity a secret to Nudist Beach.
Anyways, booooooooooooooooooo! I was really,
really, hoping they weren't going to go with the whole angst "IM A MONSTER" angle with Ryuuko prior to this episode.