It seems to work fine though i personaly wouldnt want the captured prisioners to be in my group if i was the mission maker. you could change take prisoner to, secure prisoner and let the player use the action to set his hands behind his back and kneel like tied with flexcuffs like in rainbow 6 3..
also, if the player isnt around such as he left the area without taking the prisoner, you should have him get his gun back and start fighting again. that said make sure the enemy doesnt surrender in the first place if the friendly units are nowhere nearby (IE the enemy group was hit by artillery.)
lastly, dropping ammo is not realistic, the enemy only needs to drop his weapon, you can remove the enemies ammo when the player uses the secure prisoner action. in real life if youre trying to surrender are you going to take the time to empty each pocket of ammo? nah you just will throw your gun on the ground and let them see your hands. because when i took prisoners it was strange there was many pouches on the ground around the enemies gun.
also, make sure the players squad is bigger than the enemies squad because under normal circumstances, a whole squad isnt going to surrender to 1 guy.
good work