I have watched and rewatched and rewatched the final scene of Season 6 Episode 1 and I am convinced that the clue in the scene is simply the way Lisbon is taken down. Her feet are yanked out from under her and if you listen you can even hear them scrape across the ground as she is pulled down.  there is no reason for a second person to be on the ground so it had to be partridge that yanked her down. Yes, his hands were bound but they were bound in front of him not behind him.