As much as Moff likes to play with the timey wimey, I honestly don't think he would rewrite so much of the past. I know that we don't really know much about Susans parents and the Doctors family, but I don't think it had anything to do with River or Jenny. Perhaps if they wanted to in a story they could make some implications, like what RTD did with the woman in white/Doctors mother, but just not say it outright so that fans could still make their own conclusions.
My own thoughts are that the Doctor had a family and children or whatever before he went off travelling but that we will never really find out about them in the show because it's all part of his mystery. That said though, if he was a husband and father, it doesn't say much for him just up and running from them. The Gallifreyan CSA can't be happy about that
