I already had done that, thirty years ago. It didn't work that well back then, and it doesn't now. This is because Cepheus and Traveller assume the character begins as a raw recruit and works their way up. The system doesn't take into account Starfleet Academy, and it also doesn't take into account that characters will remain in Starfleet as they enter play.
I don't see why you can't use High Guard
. Just give automatic skills for the Naval Academy, Flight School, Staff College, Command College, or whatever. If you don't want random skills, do like T20
and give so many skill points for completing each school. Remaining in Starfleet is no problem. Just don't muster out.
I seriously think this is the problem Mongoose and Amarillo Design Bureau ran into when trying to create Traveller: Prime Directive. They tried to make Star Trek fit the rules set, rather than adapting the rules set to fit Star Trek. Being unwilling to change the game rules, coupled with Amarillo Design Bureau's insistence that no flavor text can be changed, and you have problems that cannot be overcome. Thus, Traveller: Prime Directive died.
I'm sorry to hear that, but something tells me that the ADB liaison chick isn't going to miss all the pedants on the Mongoose fora.