No..he meant a child. That was not a vague reference at all. He told rose "he has been a father before"in an episode involving a child-and was very specific to donna that "seeing jenny reminded him of them of what he lost and the pain" etc, it was "specific"to refer to Jenny at that point and about responsibilities about sudden unexpected fatherhood. That was the point oif his conversation with donna at that scenes moment- that he was holding back allowing it- "when they died that part of me died with hem" would not make ANY sense if it was his companions because he has taken on new companions willingly since the time war. No--this was more specific. ADD to this, stephen moffat has gone ON record stating that he would not be against marrying the doctor,and that he feels the doctor has had many families in his long 900 years, to think otherwise is "ludicrous" its as ludicrous as us now believiing there is no possible way life could exist on worlds beyond earth, with how HUGE the universe is..no..a 900+ yr old man, time lord or not, has done things we will never see on screen, that is more than a dozen average lifetimes equivelant to us humans.
Russel t Davies once said in an interview,and i wish i had the source to cite here but i wikll look for it, that he believes that the doctor may turn out to have been married to romana during the 8th (paul macgann) doctor years,and that she and he may have had a family and they are the family the doctor is reffering to. He said in "blink" to sally sparrow he was always doing things in the "wrong order" which was awkard especially "at weddings..especially my own". There's far more than enough evidence that between all these references, and the fact it has been actuallys aid by carol anne ford (susan)in a dvd commentary that the producers always clearly told her that she "was" the doctors biological granddaughter,not a grandfatherly "figure".
I also just realised- it now makes sense why susan was not with her "parents"when she left with her grandpa- as we learned they take them away from parents at 8 to enter the academy. she may have "run away from school"not wanting to finish and be a time lady,and the doctor sympathised with that rebellious non conformist ideal and took her with him.
