Almost certainly, quite a bit later. Department Heads/First Officer as a system is fully designed, integrated, with issues worked out and much of the code worked out. Conversion of First Officers to a playable captain is an idea that has been tossed around in various conversations.
I'd imagine that the idea is that instead of the player beaming down to a planet, you'd beam down as the first officer instead (since taking a flag admiral down to a warzone is a bit risky). Thus the first officer is playable, but it's not really your main charactor? Although yeah, this isn't even in the whiteboard phase, that's just how i imagine it could kind of work. I'd say this kind of system could work quite well when the level cap is increased to go hand in hand with fleet admiral gameplay.
Any hints at how long until the system is ready for braoder testing? Also any chance the marketing guys could approve any more screenshots? :-)