You can do this by editing your mapcycle. Pull up the Config/DedicatedProfile_server/DedicatedPlaylist
file from the "File manager" page in your control panel and scroll down to the [CustomPlaylist]
section. You should see many lines starting with "Map=". Delete the ones that you don't want there, and reorder them as desired; for instance, to delete the non-GC maps, remove everything that doesn't have a game mode of "FL".
If you'd like to have a Battle Commander, add ",BC" to the GameMode bit. For instance, you could use "FL,BC".
More information is located here: http://wiki.homefronter.com/wiki/Dedica ... ist_Config