It doesn't have to do with political correctness, but rather stock price. If it comes out that Bill Gates thought this was a bad move, Microsoft shares will fall. He'd be hitting himself on the head with a hammer.
They would fall in the short term and then rise when a new CEO would be found. I doubt Ballmer would be able to stay as CEO if Gates went against him. Gates is not worried about fluctuations in the stock price of Microsoft. He's a long term investor.
You seem to be saying that if Gates didn't support the decision, then he would try to get Ballmer out. I disagree -- this isn't a big enough issue for that. (Edit: I should clarify. It is a big issue, but Ballmer wasn't acting on his own. Replacing him would accomplish little.) So while Gates is a long term investor, it still makes no sense for him to speak his mind on this at the cost of stock price. It might not affect him much, but why discourage others from investing, even the slightest bit?