They didn't want to talk about Project Mogul with a guy who had run to the newspapers with this flying disk story. Orders were orders and, with an ill grace, Marcel went along with the weather balloon story. Since they never told him about Mogul, he denounced the weather balloon story years later. It was, after all, a lie. Back in late '47, Roswell was still abuzz with the front page news about the crashed disk.
Every small town has tall-tale tellers and they'll try to outdo one another.
And so it went, the story getting a life of its own, told and retold and revised till some of the tale-tellers believed it themselves. So they had to make sure the story died. And there were known to be Soviet agents in New Mexico, since the southwest was a key testing area for atomic weapons and other secret projects. So yes, it was necessary to keep people away from the debris field, and to haul everything away to another base. But for the remnants of the highly classified Project Mogul, during the uncertain days of the early Cold War, the secrecy oath made sense.