Obviously the game only runs 1024x768
End of quote
Huh? Certainly that's the base resolution, but the game will run in anything above that. I run in 1680x1050 myself.
Now if for some reason it just isn't showing any other options (possible if you've not installed your monitor's drivers and windows only sees it as a generic plug and play display), you can set it manually in the user.setting file found in:
Vista:
C:\Users\username\AppData\Local\Ironclad Games\Sins of a Solar Empire\Setting
XP:
C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\Setting
Please note these directories may be Hidden by default. To unhide them, go to your Control Panel -> Folder Options -> View and set yourself to view hidden files and folders.