I think pedo-Dad is very unlikely. For a start, I don't think a murderous paedophile is going to stop at one child and William would have racked up quite a body count by now. Also, if Diana thought Reid was in danger from his father, there's no way she would have asked William to take him when they split up.

Either Mini!Reid is the killer or Dead Uncle Daniel is the wrong 'un. Or I'm completely and utterly wrong!