If Bernie had done what you probably would have preferred and run on the Green Party ballot line in the fall-Jill Stein offered the Green line to him- he could never have been elected, because the Electoral College makes third-party presidential victories impossible- no third-party candidate could ever, under any circumstances, win 270 electoral votes.
Bernie would have been ground between the gears of both parties, and could well have ended up being the 2016 equivalent of Henry Wallace, the Progressive Party candidate of 1948, who ended up winning 2.37% of the vote and leaving nothing whatsoever behind.
What good would it have done for Bernie to end up like THAT?