This has nothing to do with the WWE. Cena is retired and isn't active with the company in any way. This is the movie studio coming down on him and not Vince McMahon.
He's forever entwined, and since he went straight from one indy promotion to WWE's developmental promotion into WWE, it's not a general "former wrestler" identification, like others who have been in multiple big promotions. He was in Wrestlemania last year, and is too big a name to not pop his head in the door occasionally, whether for a interview, a run-in, as special guest announcer, or just "look, it's John Cena!!" just because.
Yes, the apology was about the movie, but it wouldn't surprise me if there was a phone call to Vince for some suggestions about how to handle to situation, and maybe even if it would affect those future pop ins. They still drag in Stone Cold in his Frankenstein knee braces to spray folks with beer and maybe drop a stunner here and there. Cena is as attached to WWE as he is to those sweatbands.