If AA leaves, he will get another GM job before the 2016 season. This past winter and trade deadline saved him. If he was on the market after 2014, then he may have had to wait a bit before getting his next shot, but if he leaves after 2015, then he will find work pretty easily. No way he sticks around if Shapiro gets the job.
As far as restocking the system quickly, wasn't that in large part because of the prior draft rules that got changed? Without type B free agency and an unlimited draft budget, have the Jays really been all that great at drafting the past couple of years? It will take AA much longer to fix the farm system now than it did in 2010-13.