Looks likes you've got the 'OK', with only the following stipulations...
1. In the credits, or on the title screen, include the text "Starship graphics designed using Galactic Civilizations 2 (www.GalCiv2.com) with the permission of Stardock Inc. (www.stardock.com)"
2. Remove the ships if the game is ever released commercially.
3. When the game is done, you ABSOLUTLY MUST....send us a link so we can see how the game turned out 
And if anyone wants to do something similar, they'll also have to contact our support team to get per-case approval
Thanks!