... Is this the right assumption to make based on what we know about how US intelligence and the US government works (historically)? There are any number of reasons why these people would have an interest in keeping it secret. It might not seem rational to you because you have completely different priorities and values, but that doesn't mean other people won't think it's rational to keep it secret.
The thing I'm pointing out that it's problematic to automatically dismiss contradictions to ones' argument by saying that these are explained by secret government actions when there's no clarity about what would or wouldn't motivate those actions - ie, if you assume secrecy takes care of all contradictions to your theory, you can prove anything.
A tricky thing about secrecy is that it exists to reduce clarity. If you had another sensitive way of gathering information (an insider, for example) you would not want an attacker to draw that conclusion by just sharing everything, by default. You will want to keep this motivation secret as well. Embarrassing the enemy has the lowest yield.