I am still waiting on renoth to push one last required change to the mod portal publicly. I have the code changes needed for this mod to allow for safe removal, but unfortunately, without the update of the base mod to 0.6.9, the feature I have for this will not work as is.
The only thing you can do currently is use the setting in factory levels itself to disable the levels globally and saving your game before removing this mod. (There was some code in 0.6.8, but unfortunately, when I wrote it then, I forgot to actually write the part of it that checks for this mods setting.)