I've been thinking over the whole "Jess and Mary being in the way thing" too. The only thing I can come up with, that makes sense to me, is that maybe they would have prevented Sam from using his powers in some way. Like, if Mary had lived, John and the boys would have had a "normal" life and, therefore, Sam's powers wouldn't have developed at all? As for Jess, Sam had started living a "normal" life. Maybe by marrying Jess, having kids, etc, his powers would never have been used again, you know?