Eight or so died in the Gary Mitchell issues and they brought one corpse back with them in Galileo 7.
I finally got around to reading the first four TPB volumes thanks to my library. The death toll in the "Where No Man" adaptation is actually eleven -- nine in the barrier encounter, plus Kelso and Mitchell on Delta Vega.
Thoughts on continuity and other things, with some spoilers for the comics and minor spoilers for Into Darkness
1-2/"Where No Man...": Hard to reconcile with the sequel because of the death toll, and hard to reconcile with later issues because it's implied that Kirk has been captain for "less than a year" (which I don't think he'd be likely to say unless it were the majority of a year) while later issues are set just "months" after the film. Also, it seems that the events of the story would teach Kirk more humility than he showed in the sequel. On the other hand, given how much faster warp drive seems to be in the Abramsverse, a trip to the edge of the galaxy happening years sooner almost seems plausible.
3-4/"The Galileo Seven": If anything, up until the climactic portions this is an even more slavish adaptation of the original episode than the previous story, with all the plausibility issues that creates. Again, the loss of a crewman makes it hard to reconcile with the sequel, even with the dodge I suggested above that the crewman technically died under Spock's command rather than Kirk's. Also the story has some continuity glitches -- the second part refers to Taurus II as "Makus III" and Makus III as "New Paris," and Kirk says at the end that he told Ferris that Uhura was acting under his orders even though he had earlier told Ferris the truth.
5-6/"Operation: Annihilate": Aside from the early pages, the story is a pretty significant departure from the original, and does more with the George Kirk character. I'd say at this point they decided that faithful adaptations weren't serving much of a purpose. Continuity-wise, I see no problems reconciling it with the film. And I note that Ingraham B was left off of the list of planets previously attacked by the parasites, which works, since in Prime that planet was only attacked in 2265. Evidently in this timeline the parasites skipped Ingraham B and went right from Theta Cygni XII to Deneva, explaining why they arrived 9 years earlier. They're a bit different in appearance and behavior from the flying pancakes we know, though, so maybe they're a different strain of the organisms.
7-8/"Vulcan's Vengeance": The first fully original story and a sequel to aspects of the movie, though it somewhat takes the place of "Balance of Terror." Since it's original, there are no major continuity questions with regard to Prime, and I don't see any problems reconciling it with ID. EDIT: Oh, wait, there's one inconsistency, which also cropped up in Countdown to Darkness
: Sulu has the conn at one point. Perhaps Sulu's line in STID meant that he'd never held the conn in a crisis situation?
9-10/"Return of the Archons": Okay, here we see the foreshadowing of ID ramping up, since the comic hints at Section 31 (and I couldn't resist interpreting the admiral in the opening scene as Marcus). But the story is... weird. When I first heard about the revelation in this story, I figured the idea was that it had been something that was true in the original episode but just hadn't been discovered by that Kirk & crew; but everything about Beta III in the past and present is so different that there's no way to reconcile them at all. It's an interesting alternative take on the concept, not a bad story in its own right, but too
alternative to work as part of a branching history. Also it seems to overstate just how widespread the corruption within Starfleet was, which I'm not sure is consistent with ID.
11-12/"The Truth about Tribbles": This is the "origin story" for the dead tribble McCoy experiments on in the movie, but the main continuity problem is that the characters never discover the tribbles' name. Spock Prime mentions it in the flashback scene to Delta Vega, but the others forget it for the rest of the story. Yet in ID, McCoy refers to it as a tribble. Also, the story portrays tribbles' reproductive rate as unbelievably fast compared to the original TOS & TAS episodes. It tries to rationalize the accelerated breeding as a response to the stress of a new environment, but then it should've happened on K-7 and the Enterprise
too. And it's just too fast to be metabolically plausible. (Also, while the story draws on the Star Fleet Medical Reference Manual
's attribution of Iota Geminorum IV as the tribble homeworld, it misspells the possessive as "Germinorum." IDW seems to make a habit of that -- Mission's End
misspelled Achernar as "Archernar.")
13/"Hendorff" aka "The Redshirt's Tale": Sort of an indirect adaptation of "The Apple," and it makes a point of having events happen differently. Though it's mainly fleshing out background for Hendorff and others, a nice little character story that's mostly original. No continuity issues that I can see.
14/"Keenser's Story": Mostly a flashback to Keenser's origins. Unusual for the comic in that most of it is set in the Prime universe, 3 years before the timeline split, and features Robau and George Kirk. That was nice to see, and no continuity issues occur to me.
15-16/"Mirrored": Retells the events of the '09 movie in the Mirror Universe, which doesn't make a lot of sense to me. I guess the idea is that in some alternate version of the Prime universe, Nero and Spock's use of red matter sent them back not to their own past, but to a parallel past. Yet that isn't adequately explained. I guess the handwave was that there's an infinite number of timelines in which all possible combinations of events happen, but I don't find that idea very satisfying. Anyway, since hardly any of the story is set in the regular Abramsverse timeline, there are no continuity issues with the sequel.
All in all, it seems that a number of the comics have continuity issues with ID or the Prime universe. It seems like it took them a while to find their way, seesawing from too slavish in the first two stories to too divergent in "Return of the Archons," but they've settled into telling mostly original stories built around remixes of ideas from TOS, much like STID itself was.