I've tried both methods. Sometimes nothing happens at all when I try through the launcher. If I manually rename them in the folder to disabled they then show as disabled in the launcher, but then if I create a new world, I've got the disabled mods in the game anyway.It's usually simple. Either using the tool, or manually renaming the files to add a .disabled to the end of the mod names in the directory.
I've also tried deleting them entirely, and if I'm online the launcher automatically replaces them before the game starts so that doesn't work unless I ALWAYS stay offline when I play that world or I have to repeat the whole process again.