I just go to exchange and buy green or blue ones from start (or when I have enough money).
I now have all blue BOs and Im only at Lt.Cmd.
I dont bother with white ones if I am going to replace them later anyway.
Problem is, I get attached to my BOs by spending time with them too much
Ok good! I didn't like the idea of losing all those points that they just got for a small incentive. Though it would be interesting if your BO's have a chance they could be killed and you would have to replace them or if they seen another command and wanted to "move on" to their own ship, sorta thing.
By the time you reach late Command / Captin level, you'll have enough Merits to replce and retrain all of of your BOs...twice over. It's not something you should really worry at higher levels.