I dont see why it wouldnt work.......I have often changed the landscape of politics in my SFC games. If you replace the cartels with the WYN and LDR, go into............C:\Program Files\Taldren Software Inc\Starfleet Command Orion Pirates\MetaAssets\ServerProfiles\SinglePlayer\MetaMap.........there you can change the political tensions between the empires and cartels. For example, I am playing a single player campaign.....Feds, conquest. When the campaign begins the feds are mortal enemies with the klinks, at war with the roms and lyrans, and discussing the details of an alliance with the isc.......i wanted there to be some balance considering the gorn, mirak and hydrans were my allies. So i went into said file and allied the isc with the klinks, roms, and lyrans and made them at war with the feds, gorn, mirak and hydrans......
If you have notepad (if you dont this mod is probably the least of your problems) than it should be a piece of cake.
Good luck