It wasn't that he left SBR that rubbed people the wrong way. It was the way that he did it that was taken so poorly - he spun a sob story about being exhausted and disillusioned with the series, and that he was retiring from competition. And then within three months, he has made a miraculous recovery and had signed with Tekno. It was obvious that he was lying to get out of his contract, and he had played everyone for fools to do it.
If he had just come out and said "when I signed, I signed to race a Ford with the Stones - but now that they're selling the team and switching to Mercedes, I am not confident in their ability to be competitive, and so I think that the best thing to do is move to another team", it probably would have kept some degree of respect. But he didn't, and so he is seen as a conniving and devious little so-and-so who lied his way out of a contract to avoid a penalty rather than manning up and be sporting about it.