Then again, the more stories told, the more contradictions. And Trek is a visual fantasy first and foremost: it would be a shame to see an onscreen event derided for failing to comply with offscreen material.
It was said upthread that Romulans in STXI were different from Romulans in TOS. How so? The movie ones had tattoos, but that was about it. Yet here we have a nice example of why novels don't really warrant the attention they get...
...Namely, the graphical novels that are supposed to give us a backstory for the movie (the Countdown thing) make the claim that the tattoos are signs of mourning, something Nero's folks did to their crania after losing their homeworld. But that is utterly inconsistent with the movie, where Nero appears on Spock Prime's viewer mere moments after the loss of Romulus, complete with a tattoo! Sure, the graphical storyline offers interesting drama and whatnot, but it cannot take place in the same universe as the movie. Should we dismiss the movie because it fails to comply with the comic? Or should we accept that this fictional universe is inconsistent, that is, poorly put together? Neither sounds like an appealing path to take. OTOH, dismissing the comic is pretty straightforward.
You're right about more contradictions coming in as time goes by. However, you picked a poor example IMO. For one thing, what was seen in the movie of those events were in a mind meld and therefore Spock seeing Nero with the tatoos didn't necessarily happen minutes after the destruction of Romulus. In other words, Spock skipped ahead in time from the destruction of Romulus to him seeing the tatooed Nero. Also, considering the fact that Spock manipulated or at least misled Kirk by implying that bad things would happen if the two Spocks met, it's possible that he left things out of the mind meld and misrepresented others and therefore there are no real contradictions between the movie and Countdown.
As for the topic at hand, there are several canonical explanations. One is, as pointed out by others in this thread, that not all Klingons were infected. The second explanation is suggested by the scientist who helped Phlox cure the disease when he mentioned possibly seeking a career in cranial reconstruction which would suggest the possibility that the ridges we see in the new movie are artificial. The third explanation is that a way to bring back the ridges was found sooner in the alternate reality.