I've had numerous times now where the enemy was forced to surrender, but I couldn't get them to completely submit/give up their cities etc. (That can be frustrating, but okay, part of the game, and I can see why), then to have them use their remaining armies to quickly wipe out some of my guys which had just won the siege at their last city etc. As they are suddenly in enemy non-war territory, and had just taken the city, they have a lot of movement restrictions so there's no way for me to avoid the fight, and as they often jsut dealt the decisive blow to the enemy they can be wounded. 

This makes no sense whatsoever. Surely if you get so far to "force" a surrender of the opponent, you also should be able to retreat quietly. Thinking of the EU mechanic of retreating armies where they are safe as long as they are in the borders of the state they fought against. As a general you would never accept a surrender only to have your troops surrounded immediately.