It wasn't his theory, it was that he presented it in the form of a dialogue with a character who was an obvious stand-in for the Pope, and then made that character sound like a complete idiot.

The heresy charges were an excuse to punish him for being disrespectful. He'd gotten approval from the Pope to publish; he would have been fine if he'd just been polite.

Obviously that's still petty and unjustified, but science denial wasn't the real reason for it.