Because you're at war with him assasination with an assasin will not solve your problem (as it would if you were simply excommunicated).

The ONLY solution in the case you described is force. Attack him and put him out of the game. Crush all his buildings in his provinces and then pull out of them.

In a few years (5-10 maybe) he will reemerge and you have a clean slate with him.
The pope ALWAYS will reemerge so no danger there.