In my playthrough, I've captured my rival Legatus Mamercus Cornelius who also declared himself Emperor when I took power. I have captured him and do not have any option to end the civil war when I speak to him. When I talk to nobles and advisers and ask them about the war they tell me "We have definitely been getting the better of them". Is this not enough to end the civil war in my favour? If it's important, I "rescued" him from the jewish rebels and took him prisoner myself.