For starters, joint war should only be available to allies (come the new expansion).
Also, whenever you declare a joint war, two things should should happen, one passive and one decision -- you should never get warmonger diplo penalties with the other person you went to war with (passive). Also, both the person that initiated the joint war and the person that followed should have to choose a causus belli. If you have none available, it's a surprise war and you get the normal diplo penalties with everyone else except your buddy.
Also, a lot of the other causes bellis should unlock MUCH sooner. Liberation war should be enabled from turn 0 and should give double surprise war diplo penalties if you capture and annex the aggressors cities or annex a captured city or CS.