Doesn't anybody know that too many secrets in a small space cause insanity? Really, if they just declassified the mission to the rest of the crew on their way to Duna, none of this would have happened. Yes, visiting other worlds is awesome, but possible alien contact? That would be the real glory for Kerbalkind... As for BERTY, he mentioned the first law, but what about the Zeroth Law? He can't allow harm, physical or otherwise, come to humanity as a whole, or simply as a group larger than the aggressors, through action or inaction. In short, with Rozer taking over and zapping Jeb, wouldn't he see this as wrong and do something about it?