I was thinking that this would be in addition to the crew transfers that Commander does -- I can imagine a situation when letting my XO go could be useful to buy the latest upgrade to the boat!
Also, if a career goes badly, trading all your best crew until you end up with the greenest and most undesirable men on your boat just to keep from getting a dishonourable discharge makes sense!
I agree too about keeping a man from being transferred away -- surely buying him back ought to be an option