I am a casual player, and even I believe the game needs a death penalty. Nothing overly drastic, mind you. but something to actually make being defeated have a bit of a sting.
Have the server save a snapshot of your character's stats, xp, inventory, etc every time you start a mission stage. If you are defeated and choose to respawn, any progress made since that snapshot is lost. Same thing if you leave a mission area befor completing the mission.
Also, instead of your ship exploding right away when defeated, have it appear badly damaged, be dead in space with a countdown to a warp core breach. If you choose to respawn, the ship explodes like normal, your progrss since the start of the current mission stage is lost, you are automatically kicked from the current group (if grouped) and you respawn in a new instance and have to restart the current mission stage. If you choose to wait, it gives your current group a chance to complete the mission stage, at which point your progress updates, Engineering manages to get the warp core under control, and ship's systems start coming back online.
This way, it's a matter of player choice and patience. Restart the mission stage in a new instance now, or wait in the hopes that your fellow players complete the mission stage. Of course, if everyone is defeated, then the enemy would deathblow everyone one at a time in the order that their ships become disabled, resulting in everyone being subject to mission stage reset....