The problem wasn't Pietersen not wanting to play rounders. As someone who never watches the pyjama game it made no difference whether he 'retired' from it or not, I did feel it was an unprofessional thing to do, but while he was keeping test cricket at the top of his priority list, it didn't really matter.
The problem has come when that lack of professionalism has now spread to test matches, trying to pick and choose which tests he plays in for the sake of a meaningless rounders tournament was bad, but the allegations of slagging off his team mates and coaching staff to opposing players during a match goes way beyond what can easily be overlooked. The ECB had to take a stand against that kind of behaviour, as much to try and stop it happening again as to back up the rest of the team who act with professionalism and integrity.