Units like the recons have sound Supressor. With sound supressor they have less accuracy and penetration power. In some mission you sometimes need a supressor and other times you don't need it. But you can't order your ai not to use it.
For example. My team (4 recons witout me) was lying on the top of a hill. They were not allowed to fire. an enemy (4 soldiers) team was ca 250m away at some other hill. they didn't detected my team. I gave everyone of my team some target. Then we opened fire (without me i was observing the enemys). After my team killed one of them the 3 left enemys turned arround and were able to kill two of my guys, before they died themselves. I played the scenario again with 4 riflemen in my team. this time all 4 enemys died, before they have been able to shot one time. I tried it severall times and normally the result was the same.