ouch
Yes, I am fairly certain that the space ship is destroyed if they take the capital, or is it the city which has the Apollo program?
Not sure if gifting would transfer the ship to another city, most likely that is a no.
I am sure some of the more experienced late game players can fill in on that.
I am also a but surprised they left it this late. Sad that we cannot get our MA's into position due to the cratered lands.