Wasn't that the mission where as soon as you get to the entry gate and talk to the guards to hand him over, the enemy attacks you in force from the West?
If so, I had similar problems with that map as well. There was a problem where if I tried to enter the prison, even just inside the gates, the guards would turn hostile towards me. I don't recall if the guards would turn hostile if they were shot by the enemy, the two methods I used on that map never really permitted me to test it.
The first time I did that map I had my entire team line up along the side of the road facing the direction the enemy comes in from, in the prone with weapons at the ready. I was doing fairly well, but before long the enemy just overwhelms my team by firepower domination. I kept losing men that way, and couldn't drop the enemy faster than they were moving into range to shoot back.
Then I tried a new tactic. I had my guys all run into the little guard building right outside the gates. Half of my team ran into the room off to the side, and the others waited at the far end of the hallway right outside the door to that room. This meant that my team was not visible to the guards, and we weren't technically inside the base, so I never took fire from the guards with that method. The enemy rushed the building, and would send in 2-4 guys at a time through the entry but they just got mowed down by my own 2-3 waiting at the end of the hall. When the enemy stopped coming in, I'd creep a trooper down the hallway inch by inch until I could finally see them hiding outside. Then I'd rip off a few rounds, and sneak back in. I was able to take them all out that way without much injury.
As for the enemy shooting at you on the mission, their hostility towards you is higher than their friendship level. Let's say it's put into numbers. Their friendship with Miguel is +20, and since he is part of your group that adds +5 friendship. But their hostility towards you is also -20, making their overall hostility towards you -15. But that +5 friendship might still be seen by the guards, so when they are injured they become hostile to anyone on friendly terms with the enemy. That's just a hunch of how it works, I could be way off. But that's what it sounds like.
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