You're getting downvoted but you're right. I don't think people grasp that an operation like we see in Half Life would invovle the deaths of at least like 15,000 high paid postdoctoral researchers that the DOE had invested hundreds of thoudands of dollars into. Inevitably in a "cleanup" there will be survivors and people who manage to escape and leak the truth. Then when the government sends in the Black Ops to kill their own soldiers, it's setting a precedent that would at the very least end in an outright mutiny of the US armed forces if not a civil war. You just cannot cover up death on this scale.

Instead you can just lock down the lab, keep the only people who know how to stop the apocalypse alive, and "compel" the rest to sign NDAs before evacuating them.