So did Courage get kicked off Star Trek because he was angry (at least for a time) about GRs lyrics or did he quit?
Look maybe Courage forgave GR in the end. Maybe he's not the sort of person who carries a grudge unlike myself. Maybe he made more money off Star Trek in syndication than he ever thought he would so half of what he should get was 100 times what he thought he ever would get for a 3-Season TV show.
Courage was not kicked off Star Trek. After he recorded his score for "The Naked Time," he went over to 20th Century Fox to adapt and orchestrate the music for Doctor Doolittle. It was a huge-budget film and he thought it was the better career opportunity at the time. But he got no screen credit for his work there, and the film did nothing for him. He later said it was a mistake to leave the TV series.
There's no evidence he was ever furious at Roddenberry or left in a huff. He seems to have accepted the lyrics grab as a lump he had to take. At some point he admitted he was annoyed that the lyric was poorly written, from the standpoint of how awkward it would be to sing, with its syllables and emphasis in the wrong places. If GR had actually collaborated with him, he would have kept that from happening and possibly gotten a decent song out of it.