This is to prevent you from forcing the emperor into multiple wars against the same person. The game does not like to have one person fighting one other person in multiple wars.
It would be kinda cool if you could declare an end-the-empire war, which would name the emperor as wargoal and every elector as co-belligerents, and possibly call all members in as normal allies.
Don't. Just more tools for the BBB to color Europe in it's color.