Didn't RTD say in an interview or something that he liked to think that Frobisher was a descendant of Caecilius and that his death was history catching up with him, or at least I think I read that somewhere. He doesn't have to have anything to do with the Doctor at all.
A big theme this series seems to be that the Doctor's actions have consequences. Ripples and tidal waves, etc. The Doctor saving Caecilius and subsequently creating Frobisher could tie in to this series, and his face could be a reminder of that. He saved the kid that grew up to be Davros a few weeks ago.