There are several other possibilities. For example, Balthar may actually turn out to be a messenger of god. 
Well, Starbuck * is * the best detective in the fleet, you know.
In all seriousness, I never got the impression that the cylon detector was that compartmented. They discuss it at least tangentially in CIC, which would never happen were it super sensitive eyes-only need-to-know stuff.
Well, a bug can work one of two ways. It either broadcasts or makes recordings. If one broadcasts, it should be detectable. If it makes recordings, somebody would need to maintain the bug, and the cylons would not have information in real time.
Still the possibility is there.