The novel surprised me in a couple of ways. For one, prior to his defection, Blair came off as a pretty weak character. From his assignment as the Lexington's wing commander, Blair seemed to play only a minor role in flight operations. Eisen had full authority over missions. In fact, Blair did not even learn about the operation in Tyr until Eisen briefed him along with the other pilots. What was he doing this whole time? He obviously wasn't involved in planning.
Later, during the operation to capture Eisen's shuttle, Seether suddenly shows up and attempts to usurp authority. Blair would have been well within his rights as both mission commander and wing commander to blow him and the other Project Hellcats out of the sky.
When hinted to Paulsen that he saw Seether come onboard, he danced around the issue as if he was afraid of what the captain might do. Instead, he should have confronted Paulsen directly. Paulsen may have held seniority as captain of the ship, but they were both the same rank (o6). Also, Blair could have asserted that everything involving flight operations (from shuttle landings to dispersing the maintenance crews) fell within his jurisdiction.
All in all, it seems that if Blair would've used his authority as wing commander, or at least his prestige as a famous war hero, the situation might not have escalated to the point where he would have to defect. Why did he act so timidly?
