Part of it was due to likenesses, they would have had to licence the 2nd character.
They also had no choice when it came to the Eighth Doctor, since Grace didn't go with him - although they did bring her back for a couple of stories that gave her a fascinating post-TV movie character arc, while at the same time anticipating Torchwood by several years.
In the case of Grace,
DWM didn't license the character, and they were told not to do it again, which is why she goes unnamed in "The Flood."
Similarly, DWM wasn't allowed to add in new companions for the Tenth Doctor until the post-Journey's End era, and even then they made it clear that the Doctor was Majenta's hired business associate, with no actual companion relationship. (IDW played a bit more fast and loose when it gave Ten a pair of companions in a story arc set right before Waters of Mars).
What's so "fast and loose" about the Doctor traveling with someone between "Journey's End" and "The End of Time"? Why do you feel the need to say that? Is it because the Doctor says in the year of specials that he travels alone, turning down (as an example) Lady Christina when she wants to board the TARDIS? If you've read the IDW comics, you'd see that the Doctor upholds the spirit of that, and only takes Emily and Matthew when forced. (The reference made to Charlotte Pollard in the second story arc wasn't gratuitous fanwank, it turns out.)
Emily was a great companion. Her story, especially how it ends, is heartbreaking.
I can see why the BBC might have been reluctant to let TV companions appear in the strips at first. For those who follow the "inclusive canon" model it can be a bit tricky to explain the Sixth Doctor's recent Big Finish audio adventures with Jamie McCrimmon, after the DWM comic strip had a "younger" Sixth Doctor witnessing Jamie's death...
You
really think that, in the 1960s, when the comic strips began, that the BBC arsed themselves about making continuity line up? Really?
Also, there is a difference between canon and continuity. Canon is a simply body of work. Continuity is which pieces of the canon fit together and how they fit together.
Didn't the DWM strip kill off Ace at one point, too, throwing a spanner into the Virgin New Adventures continuity?
Yes, Ace died in "Ground Zero," which sets the stage for the first two years of the eighth Doctor comic strips. It didn't really affect the New Adventures, because they were winding down at that point, and Mike Tucker wrote a PDA for BBC Books (
Prime Time, I think) that mostly reconciled the whole thing. No, the real issue was that it munged up the comic strip's own continuity which, round about '92, tried to correspond somewhat to the New Adventures, only now the comic strip was contradicting itself.