I know what you mean adamoneil, if your enemies are guarding the hostages and they are fired upon, they will shoot the hostages.
I only had success with 3 approaches:
1) Realize this is probable very realistic behavior on the part of the enemy AI and incorporate it into the mission.
2) Face the enemy guards away from your hostages, thus allowing the Ghosts more time to eliminate the guards
3)Seperate the guards an the hostages by a room, wall, big rock, tree ect.
4 (Oops 1 more ) Make the hostages invincible,
There is probable a way to play with the AI of the guards thru scripting but, I am not familiar with it.
I do know that normaly Enemy AI will shoot hostages when a threat is detected.
Wwoody