I've never liked the fanon Shep-backstories that involved abuse or inexplicable ostracizing. Pasts like that would have made for a very different John Sheppard. I'd always felt there was a combination of love and tension in the household he grew up in - one that taught him how to care while at the same time made him wary about forming attachments... or something along those lines.

So (according to all the many spoilers I've been reading) his past makes perfect sense.

And like I said on another post - Ha! No fodder for the anti-kirkers! John didn't have an affair with another woman!