I'd always thought the reason Isshin left SS was because of Ichigo. I'm sure there must be rules against having a child with a Quincy (enemy). I had always assumed Isshin was simply in hiding on earth. (Though I digress, previously it was because of Ichigo being his son, and not entirely of "what" Ichigo was.) (As Ichigo being a Quincy/Shinigami hybrid would likely have been killed had his existence been known about by SS)
Also, I thought it was mentioned earlier that the Quincies confronted Aizen to recruit him to their side in this conflict and he said, "yeah, no thanks guys, i'm good all bound up here for now."