Wouldn't it be protected under usage as a parody? Unless they directly claimed characters and concepts from Dr. Who and imported them all into MLP, a passing reference wouldn't result in legal recourse---unless the copyright holders of Dr. Who really had it out for MLP: FiM.
We had "The Return of Harmony" ending which was a frame-by-frame reenactment of the ending of Star Wars. Of coruse, tomorrow we will see at least one other blatant parody of a famous science fiction film. I don't know if they would be held accountable for the direct references.
It really depends upon what exactly they choose to do. If they go the route of parody, such as having the Doctor make a joke about being just the Doctor, or having him quote the wibbly wobbly timey wimey stuff bit...that might be okay. I'm not sure how often Doctor Who is parodied by other shows or how the BBC reacts to such parodies.
But the thing is, I can't see them even doing that much, because Hasbro operates under a general standard of being as careful as possible, even if they do allow the show writers and makers a lot of leeway. After the Derpy Debacle, I don't expect the show writers are going to be able to get away with nearly as much as they were able to prior to that. It's the same reason we'll never see a canonical acknowledgement of same-sex couples, of background ponies or other characters.
It's a little different, parodying a sequence of events such as the Return of Harmony ending parodying Star Wars, and having a character parody show up. Character parodies are always much more tricky to pull off without stepping on toes.
I mean, if they did do it, I'd be delighted. While I don't watch Doctor Who yet, I plan on getting into it eventually, and so seeing a parody of it on the show would amuse me, much like it would plenty of Doctor Who fans. I'm just not seeing it actually happening.
But, as always, I could be wrong.