If I can't uninstall a mod mid play trough it pisses me off as well. I usually delete them permanent if they are not important enough. If you keep adding and removing mods from your save games soon or later it will prob crash. However there is a solution for that. After removing mods if you don't have imediate ctd and your savegame is corrupt your can pretty much fix everything. Just make sure to use fallrimtools or another program to clean your save games every once in a while. This should prevent data of unused mods piling up.