Joss had lots of involvement in seasons 6-7. Many of the 'controversial' plot points that the fandom was harping on were his ideas, he signed up for the rest of it, he rewrote some scenes and when he didn't have the time to write the dialogue, he gave the writer notes to follow them (the latter is what StevenDeKnight says he did for Dead Things). Everything points out he was doing exactly what he wanted. He always had more a lot more clout than anyone else in the show, including Noxon as the nominal showrunner.