The sentry targeting code was chosen for specific game play reasons... going all the way back to q2. The sentry was never intended to be "intelligent." It was a tool. If it intelligently prioritized people grabbing the flag, you wouldn't have the strategy of sending in a meatshield first to "tie it up"
Hell I didn't even make this decision... it was made all the way back in q2 and people freaked out when we even considered "fixing" the way it worked. Remember all the drama over being able to duck to avoid sentry fire?
People have short memories. :)