I honestly don't recall anything in SG that alluded specifically to William. It's entirely possible Miru decided to keep his child even though they were no longer together.
And then there's also Miru's unnamed sister in the old WIAB. I'm not sure if it's been made clear or not that Ayua is Miru's child or niece.
Basicly you are right, that is the the reason because i have written "til now" in my post. Still, the odds are pointing towards my guess. We can only work with that facts that we already know, and that are the events and persons that apeared in the old WIAB.
In SG Ayua point out Katie Zane as her aunt, that means that Willian is the father of Ayua. An with that what we know, till now, it is very unlikely that William has a offspring with Mirus unnamed sister - but your point still not impossible. The game itself was till now complicated enough, other reasons would make the game much more complicated.
The story of SG and WIAB needs a common canon storyline and with the information we have, it's most likely that William and Miru will stay together. Of course, this is all just theory and Ocean can still say "fuck you all" and pull another story out of the hat. Personally, with the usable information we have from both games, I think this is the most likely set-up.