So, Saul and Lizzie have been separated for roughly 5 months (or, at the time Saul discovers Lizzie's condition it's been about 4 months. As pregnancy goes and 'showing' anything less then 4/5 months, she wouldn't be showing enough to be called 'not so skinny'.). If Scratch has been protecting Lizzie since she was almost raped, I don't see much of a chance that the child could be anyone's other than Saul. So there is my vote for that.

My vote for Saul rocketing down to the colony is a definite 'yes' especially if he believes that the baby is his. There is no way that he's going to sit back and let her stay there with his kid.