Actually, this is not completely true. ThunderStore manager is pretty good in giving you all the options you want.
1. You can singularily en-, disable mods.
2. You can start modded.
3. You can start plain vanilla.
4. It will look for recent updates to mods and offer you to upgrade them for you.
5. And last, but not least, you can uninstall mods as well.

I can't think of any better way to handle mods. Unfortunately, most people don't seem to use it, or we would experience way less calls for help in here.