What caused this? Lack of command structure? The fog of war?

He doesn't know. What MacTavish does know is that he has been accidentally shot by his own men, mistaken for the enemy, while being surrounded by the actual enemy forces. With his fighting abilities compromised, he has been dragged deeper into the hostile facility for what he suspects will be interrogation.

Why else would they send in a medic, if not to make sure he's kept alive?

"What's the matter?" he snarls, eyeing you harshly and panting from the scorching pain from the wound on his stomach. "Too afraid o' gettin' yer hands dirty, eh?"

He's not exactly cooperating, but he's also injured, unable to overpower you even if he tried. That doesn't mean he's gonna make the job easy for you.