So, you have a victory condition like "You must build three castles to win" but players can circumvent it by just killing the enemy entirely. Is that right?
Well, you don't really need a dummy computer player. You could hide a single unit from one of the existing players just as easily.
However, you should give some thought to the design of the scenario. Is your scenario's goal sufficiently involving that the player won't even realize that the enemy players are dead because he or she is so busy completing your quest? If so, then there's nothing wrong with the "hide a unit" solution. I never noticed when Red was left powerless in Mia's catch-the-sheep scenario, because it just wasn't important at that time.
However, if the player is going to feel like he or she has accomplished something by defeating the enemies and will then view finishing the quest as a chore, then you have a problem. "Oh, right, I have to build six barracks. Sigh."
If that's the case, you might consider strengthening your enemy so that some inner sanctum remains very difficult to beat. This will provide your player with incentive to reach victory in the way you've planned.
Yogurt