Well, it would have to have been someone he could make an association with in his timeline (so not some random woman he meets in his future, but something related to what he's already done), so makes sense that it could be a companion's kid.
I also had the "eh? she's not his mum is she?" thought, but they definitely kissed in a romantic/intimate way previously.
He seemed so happy that River was Rory and Amy's kiddo. Bless him.
Will river be calling Amy and Rory mummy and daddy from now on then?