SPOILER ALERT (Season one though...)
When the fleet first escaped, Baltar made a Cylon Detector out of a nuke. The first person he tested was Ellen Tigh, on order of the President and the Commander. The second person he tested was Then-Commander Adama. Granted, the tests were frauds, but they resulted in both character's innosence being "proven". From then on out, the vast majority of the other characters laid down their lives for Adama, the few who did not were either Cylons themselves or seriously messed up in the head.
END SPOILERS
Wouldn't it be possible to have Baltar simply look at the Admiral's loyalty cards and see wether he/she is a Cylon or not using the Cylon Detector ability? Most likely, this should be done as soon as the sleeper phase hits or the first Cylon (in bigger games) reveals. Baltar then tests the Admiral. If Baltar isn't a Cylon, he has no reason not to tell the truth. If he IS a Cylon, since the other one already is revealed, then it can't be the current Admiral. The only thing he gains from lying is the loss of 1 morale and his futhre execution.
Baltar is not a Cylon, the Admiral is a Cylon: Baltar reveals the Admiral's guilt, and he is executed. You now have a non-Cylon Admiral.
Baltar is not a Cylon, the Admiral is not a Cylon: Since they can not both be Cylons, you can assume Baltar is telling the truth.
Baltar is a Cylon, the Admiral is not a Cylon: Baltar says the Admiral is human, and it makes no difference becuase he isn't a Cylon anyway.
Baltar is a Cylon, the Admiral is not a Cylon: Baltar says the Admiral is a Cylon, and he is executed. Surprise, he's a human! Baltar lied, and you execute him.