He seemed to imply that he chose not to kill Alduin. "I chose a different path," he says (if you had already slain Alduin). What path was that? BTW, was he ever really dead or just waiting in Apocrypha? If the dragons killed him, it kinda casts doubt on his capability to slay the dragon god.
He did die. But HM claimed his soul due to the deal of obtaining the forbidden knowledge. He sought to escape his fate. Hence being BF'ed at the end by a PO'ed Daedric Prince.
Edit: Also, technically you can die any way, falling off a cliff, etc. I don't think being DB implies impunity from death by dragon. Don't forget you yourself had to have the help from 3 others in Sovengarde, and even THEN, you still didn't permanently kill Alduin.
Edit two: It is possible he schemed it all from the start. Knew that he could escape his duties as a DB by being Herma's servant. Waited until the time was right, and, well, try to escape after you did his dirty work.