It's a wish-it-was article. Radical Republican reconstruction had been installed in place of Johnson's milder version. Lee opposed the radical reforms and supported Seymour in the elections. Lee felt his place was more as a sort of conscience for people - his duty being to help all he could to put things back together and heal hearts. Although he never said so, it seemed a religious endeavor as well.
At any rate, Lee wasn't a citizen. He couldn't run for office, be drafted or anything else. There was a reason the citizenship application got lost!