Someone on the comments page made the interesting observation that 2.5 might die, and that got me thinking... who could be killed off in this comic? (Not that I want anyone to die! I'm just wondering what's possible within the comic.)
2.5 is an illusion, so he can be killed/disappear/be reabsorbed into 2. Also, as an original character, it won't disrupt the timeline if he dies because he doesn't appear on the show- there are no stories he has yet to appear in. Same applies to the president and the other unnamed gallifreyans.
The other doctors can't die because they all need to return to their timelines and continue with their on-screen adventures. Well except 8... I always assumed that 8 died in (or during) the time war, and I think his appearance in the comic is from before the time war... but since he isn't shown regenerating on screen, and his dying in the war isn't canon (as far as I know) it's possible he could be killed off.
As for the companions, I'm pretty sure susan, jo, romana, tegan, turlough, peri, rose, martha, sarah-jane and the brig are all taken from a point before their last onscreen appearance, so none of them can be killed off. (So is jack, but you can kill him as much as you like. Jack comes back.
I think rich said jamie and zoe are taken from season 6b (correct me if I'm wrong!) so they can both be killed off. I'm not very familiar with nyssa and mel but it seems like they are both from some point after their last appearances, so maybe they could die as well. And we never found out what happened to ace after survival, except that she was no longer with 7 at the start of the movie. She could die too. So could leela, since she's clearly much older than last we saw her on tv.
As for the other characters like the rani, the k9's, drax, davros, glitz, and everyone I've forgotten, well I dunno. I'm not sure from what timeline's they are from. Any ideas?