Yes, he absolutely was.
Except that's what happened. You keep telling me that what happened didn't happen, and that's never going to work, because it did happen. He was having thoughts. You call it protesting, but that protesting consisted of thoughts. You have not once shown how his protest consisted of anything other than thoughts. You have not even alleged that the protest consisted of anything other than thoughts. The fact that you call it a protest doesn't make it not thoughts. It was still thoughts. And he was prosecuted and convicted for those thoughts. The excuse is that those thoughts constituted a protest, which may well be true, but it's still a prosecution for thoughts. Which means it absolutely was a prosecution of a thought crime.