Limiting it to the enemy makes it stand out even more that the enemies are arbitrarily made to be harder to kill than the mercs. That’s a bad thing, since it undermines the equality between units regardless of what side they are on (a bandit is not fundamentally different from a merc).
I could only see prisoners work with the current system if the healer-companion gives you a chance of keeping some enemies alive. That way you side-step the issue of death states, since the point of the healer (last I checked) is to give you a random chance of saving a merc who gets killed (but with an intact body) in battle. You’d just be applying the same mechanic to the enemy as well for the purpose of taking prisoners. You also avoid the problem of wanting to target certain units and save scumming, because you simply wouldn’t be capable of doing that. A deeper system would otherwise require creating a lot of new mechanics to make it work.