This is an issue I hope the developers are looking at. I've also had to turn off cloud syncing to delete custom factions, sovs and unts, and even then, having to sort through files to accomplish this is quite a hassle. I very much like the idea of customisation, it's one of my favorite elements of the game, but the feature can't be WAD, and if it is, the design seems faulty.
Stardock, we need an effective, simple interface to delete any and all custom creations, without having to tinker with the files themselves. As this is an advertised feature of the game, this should be fixed before release.