You may want to look into having units that can capture others, but have the other unit still be somebody elses (not just for animals) let me explain:
A hunter can use a net, and effectively ambush a unit and hold it prisoner. There would be a rather low success chance, so as not to imbalance... and the hunter can only capture units by ambush (of course, I'm 158% sure that you probably wont do this, cause you lik's your hunters the way they iz), which means they would need to have the abiltiy to "hide" this should only be avaliable in forests and jungles and hills (maybe not hills). This turns on invisiblity, but is like fortify in the sense that it goes away if the unit moves. From invisible mode you have many options, you can capture, ambush (higher attack), and cast certain spells (like the illusion spell, hehehe... but not fireball). This could add new gameplay (although the AI would use it like a fish uses a pen).
Some stuff on captured units:
When a hunter (or other unit) takes another unit prisoner, the prisoner must be dragged (similarly to animals) back to a city. From there, the unit can be used for all sorts of things (some a bit unsavory). You could just store the unit in the city, but happiness would go down (unless you have a courthouse, or jail or whatever) I'm not sure what bonus you would want to give, but I'm sure there is some kind. The unit could, with a colloseum, be "expended" for happiness, and some culture as well. You could take the unit to your capital, and then trade it back to the original owner (or one of your allies, hehehe...). Once you have three prisoners in one city, you can build in that city a "prison ship" (unit) or a "jail wagon" (unit) or a ("?") (permanent building). The building would have some kind of positive, while the two units have a different purpose. With the prison ship you can move your prisoners across the water, to different places, and then release them (they then become barbarian, which can help you gain XP). The same with the jail wagon, but on land. I'm not sure, but they could be used for different things as well, right? (it is dark fantasy)
Just a suggestion, I don't know how well it fits into your mod...