In the end, John Proctor himself has been accused of witchcraft. He refuses to confess and is sentences to death. He did tell Abigail that it was over between the two of them and ask for Elizabeth's forgiveness. He didn't confess because he didn't want his name to have a bad "name". He also didn't want to teach his kids to lie by having to "accuse" his friends of being witches if he does confess. He doesn't want to leave Elizabeth and his kids but he wanted to do the right thing and be a honest person.
I consider John Proctor to be a really good person at heart, everyone does make mistakes in their lives but it doesn't mean that they aren't a good person. One of the dictionary definitions for stooge is one that is used by others. If you use this definition, John Proctor can be called stooge. His friends are technically benefiting from him not confessing. They're not going to be accused of being witches! His kids also won't have a bad impression on their name. This is why John Proctor is both good and a stooge, but mostly good.