I've managed to play a very stealthy character so far, avoiding firefights and direct contact with the enemies, but now I've run into some problems. I'm currently in Paris catacombs, near Bunker 03, where Silhouette prisoners are held.
And here comes my question. If I release the prisoners without eliminating the guards first, do they get killed?
It's been a while since my last DX-run, so I might be wrong. But yes, most likely they will die. I believe they will just run to the hideout, which will of course alert the MJ12 troops who'll start firing. I think I let that happen once. You'll probably get your Skillpoints, but it's not the proper way :)
If you want to avoid frontal combat, you can probably take them out one by one with a sniper rifle and some gas grenades though (or shoot the toxic barrels with something silenced when they are near).