If your ship is about to go boom, there should be the following options:
1. Emergency Saucer Seperation.
2. Evacuate all personel via escape pods.
3. Wait for a Starfleet rescue team.
4. Return to Starfleet Command and get reassigned to a new starship, but not be able to modify and or rename it until you acquire a certain amount of XP.
For those who prefer a stronger Death Penalty like Demon's Souls (PS3):
Now if your Starship is out numbered, and you think what would Kirk do.
1. Set your Starship to self destruct mixing the Matter / Anti-matter chamber ant take all your enemies with you.
2. Start a new character.
3. Play a minigame at Starfleet Academy called the Kobayashy Maru. If you can beat it, your charcter gains the same rank as your previous character that died in battle.
I actually really like the escape pod idea. You could respawn with a minimal crew and then go collect them again.
I'm just not sure this game is really "equipped" for losing your ship though. The respawn doesn't really bother me, I like getting right back into the action, but I still understand the penalty idea (I studied game design, come on). The respawn offers nice gameflow, anything else would hamper it. Restarting the already quite repetitive missions doesn't sound like a good idea, either. Death should still be desirable to avoid. I like the saucer separation/escape pods ideas. Then respawn and collect them. That's a quite immersive penalty and it's not too frustrating.
Maybe I've been "quicksave spoiled", but I don't like losing progress because I died in a video game.