I think its to limit expansion. If you know your stronger than the coalition and declare on them and separate peace them for full annex or take max land from them then it removes them from any future coalitions or weakens them to the point that they won't be able to form one again.
Its like having a large France getting collationed by half of Europe you could then declare on them and just stay at war for years annexing nation after nation until you get to the point where no other coalition will form in Europe because your just too big and strong for them to even be a threat to you.
Coalitions are meant to be more of a expansion block for those who become too aggressive. They are a punishment for expanding too fast and if you end up in a coalition war the war itself is meant to slow you down.
I do agree that you should be allowed to separate peace each nation once you at least occupy their capital or have a decent amount of war score but only for war reps/money etc and not for taking land from them. Its very unrealistic when you fully occupy a nation in a war and they can't peace out until the leader accepts peace.
Edit. I've had a coalitions form on me in a few games, mostly in Europe when I see a chance to force PU someone large and don't wanna wait for the AE to die down but I will normally improve relations and try to get them to disband. Only ever fought one coalition war and I won it after 12 years, many loans and the loss of all my manpower but it feels good to win a war as a defender when both you and the AI know you would not normally have won.