In the spirit of the Chekov arguments here, he could have been replaced with, say, Dumbledore's twin brother, who was the actual mastermind behind the whole "protect Harry" thing. Then they could add a throw-away line that the real Dumbledore was off on some magic soul-searching walkabout, or exploring the galaxy on the Reliant ,or something like that....
After all, people would complain if they dared to replace him. That would be disrespectful to the great Richard Harris!
We can argue about this all we want, but at the end of the day it will be Paramount that decides whether or not Chekov appears in ST4. They own the characters, not JJ. All it will take is for an exec to say "No, Chekov is alive and in the movie" (not unlike the way Uhura said "No, I'm assigned to the Enterprise." in ST'09). As with Spock, JJ and co. will really have no choice if they know where their bread is buttered.