As in every game or sci-fi you will have to go into it with some pre set notion of how the universe work that does not correlate with reality... such as a universal time frame and FTL communications... otherwise things would not work.
Sure it will work, but not as RTS gameplay anymore.
You create a fleet, give them orders what they should do and then they either report back with a fast courier vesser and wait for new orders from that courier or fly back to the HQ.
Basicly the same like at the good old times, when sailships are on mission for years at the new world.
I got once a game with this, LONG time ago.
But while they wait for new orders from the courier, they need to sleep at cyrocaskets.
Yes, it's been done before on a board wargame. It was implemented differently than you suggest though. You are correct, it cannot work in a real time game. I always like the WITP/AE model, turn based planning, real time combat, that would work too.
I will do what I can to mod DW2 when it arrives, maybe I can get some flavor of this in the game.