If you have the earthling cruiser you can beat it with a loss of a view men. You just have to make sure your ship starts far away from the probe. If it does you shoot two missiles and use the close range things (I do not know what the are called) to take out the last crew. I was stuck like you until i got lucky and did that. If you do not have any ships then you are screwed because the single ion bolt gun is very hard to aim (at least it is for me),.
So I have read that the reason the full screen hd display is not working for me is most likely because i do not have a high enough resolution screen and I have also heard there will be a patch that allows it in different resolutions soon. I was wondering what would happen to my save data if I updated the game when it came out. I don't want my saves to be deleted is all so if my worries are not needed please let me know.