What happens if that unfortunately scenario occurs?
I have three possible solutions:
1. You lost your avatar forever during this game. You also lose all benefits of your killed avatar.
2. The avatar's ship is destroyed and the person (avatar) has escaped with small shuttle (with 50 shileds HP, lets give him opportunity to escape from the battle). Now you can build another personal ship (it will cost you a lotta money) for
your avatar and transport it back. If the avatar ship is destroyed and then his shuttle --> see solution 1 or 3.
3. You can respawn your avatar for a reasonable amount of time and resaurces like in Warcraft 3. (Unrealistic one)

I personaly vote for solution 2 and then 1.

Well, this defenitely answers a few questions. I quess I played too much warcraft3 with their Heroes type of RTS. Anyway thanx for info.
Oh, one more question regarding this topic.
Did you considered (maybe in future betas) bringing avatars with their personal starships into the Fleet Ops. ?  

I think in later betas it will be cool to have them.  Maybe they would have a special weapon only for that ship.

The real role of our avatars with it's ships (our Heroes) should be the role of flagships in our fleet and lead other ships in battle. Optec said that when you choose one of them you get some benefits and you can build new class of starships. Well, the benefits shouldn't be just special weapons but something else
(for example all your cruisers are faster for 10%, or all attacks against The Borg
are 20% stronger, torpedoes are more accurate and faster by 30%....).
This Admiral type of avatars (Heroes) can be seen in game Conquest: Frontier Wars or Warcraft3. In CFW you choose your admiral ,you get him in the shuttle, then you transport him to one of your's larger battleship. Your fleet is now stronger then without him and you get the benefits already described.
Can this be done to Fleet Ops. in any further release?

It would be great if it could.

That's fine with me.