I had a similar problem, not with the terminal at the turret room, but with a couple of terminals over the enclave (basically all terminals offer the same options), they stopped working when I tried to activate defense protocols without the passkey, so you might have to load a savegame BEFORE entering the Enclave.
There's another issue (a bug actually) which isn't even fixed with the patch. you may have found that there is no option (or it won't react, I'm not completely sure) for counter insurgency. The problem is fixed by selecting "retrieve help file" and then selecting "yes" when asked to update it. The counter insurgency protocol should work now, provided you have the presidential passkey
Hope this helps a bit
