The Eighth Doctor infamously refers to himself as half human in the TV movie, though that has been largely ignored in the new series. The only times it does get acknowledged is when they want to make a joke ("Are you human?" "Is that optional?" "It is for me.")
Since the Timelords have the technology to make a Timelord into a human...couldn't they make a human into a Timelord? (In fact, on fan notion was that Ace eventually went to the Timelord academy, and because a Timelord - though that fanwanky idea was contradicted by dialog in an episode of The Sarah Jane Adventures...)
It's possible that the Doctor's biological mother *was* human...at one time. Or, the Doctor could have a a human mother, and yet still be 100% biologically Timelord.
I know that the show will probably just ignore that line in the TV movie, and never explain it (then again, some day a new producer could come along who wants to explore it)...but the line *was* said, and in my own personal canon, that's how I explain it.
Plus it's Doctor who, being "part human" and "half human" can mean lots of different things. (Maybe somehow during the regeneration that Doctor was contaminated with Grace's DNA, and she's his "mother", lol. Or maybe he was half-human for *one* regeneration - he also said in the movie that he could change species via regeneration!!)