I say, go the innovative route and minimize the amount of death or chances of death. When player characters (not NPC's or MOB's) are defeated, they are knocked out or incapacitated, not killed. Yes there are Phases and Disruptors set to Kill or Disintegrate; but how often were the main characters (which are player characters) killed? They somehow got through it, mostly with hits to the shoulders or having that doctor nearby or in time. And if there was death, there was always a way to cheat it.
So a death of a player character could become a mini-game in which the player must figure out the way to cheat it. Remember that episode of Piccard being killed and chatting with Q in the afterlife?
As for ship battles...
Ships have many systems and do not have general hit or body points. But no one knows how that will work... Ships I would say are not the same as characters. Ships can be destroyed and lost. Thus players should be careful with their ships and retreat from battle if the odds are not good. But what happens when the ship is lost?
The player character and some of the crew manage to get to the life-pods and get rescued or captured (another mini-game to try to escape) and once again avoid death. When the character returns to duty, another ship is provided (we won't worry about the realism of captains who loose ships get a desk job), though more of the standard stock.
That's my take.
Be different, be more like the shows and movies and make death of characters a rarity. Why do computer games have to have so much death and senseless killings eh? (Oh to make Ensign or to raise my Phaser skill I need to kill 100 wombats).