The reason to me is also not clear. But as far as I know the marines failed at their task, and thus the black ops had to be called in to detonate a nuke and kill the remaining scientists and marines.
Or maybe it was supposed to like that from the beginning, but then I don't understand why call in the marines, why not just send the black ops and detonate the damn nuke. Maybe the G-man wanted as much earth foreces to die so that the alien invasion might be easier.
As soon as the thing happened, the black ops were probably already going to be sent in to nuke the place, but because the marines screwed up, they came in to finish the job sooner. (but not)
The marines were sent in to clean up the mess, but they really just made it a lot worse. In order to take care of this the government sent in black ops after them to kill EVERYONE (witness's) and nuke the building to prevent the aliens from spreading out of it. I don't believe that they initially planned to nuke the building, it was a last resort.