In SFC, you are correct, Karnak, missions are played at sublight speeds. I don't follow your argument about the impulse engines having to be shut down when leaving warp though. I don't recall the Enterprise coming to a complete stop whenever it came out of warp. If you want to quote other science fiction, another good example is from Babylon 5 where ships coming out of hyperspace, whether it be using their own jump engines or a jump gate, were always at speed as well.
DieHard does prefer to start missions at speed zero, true, but this preference is based purely on game balance and a focus on PvP. DieHard would be happy to have just a few patrol missions and the necessary base and planet assaults and prefers the 'drama' of the game to come from PvP. This is fine if you like PvP, however, a lot of players also like to run interesting missions as well, and to play the same old patrol 50 times in a row to flip a hex can be become a bit tedious.
If game balance requires that the ships be started slower, then that's what we have to, but I want to explore other avenues first. Since not all other avenues have been exhausted yet, it is premature to have to go back to the normal mission start with speed zero (which I always thought of as odd, unless you are sitting at a base or something and it makes sense in the context of the mission itself to begin stopped in space). Since the 'speed' bug is no longer an issue, we can freely start missions with ships at speed and in my opinion lends itself well to many missions and makes the mission more realistic. It is just a question of game balance, hence the need for testing.