What happened to Bon Clay after the Impel Down arc?
Bon Clay did not get killed. He somehow survived the fight against Magellan, and escaped to the Level 5.5 (Newkamaland), where he has become the new "Queen". Many of the Newkama prisoners who escaped during the Impel Down arc have reoccupied it.

The canonical evidence is on the cover page of Chapter 666. It is not yet known how Bon Clay escaped from Magellan, or how and why the Newkama prisoners returned to Impel Down.