How to disable all commerce modules from Commerce Kickstart using Drush?
Note that by disabling all of the Kickstart specific modules (which is practically required to uninstall Commerce due to dependencies) may cause your site to become unusable. If you're using the image rotator or the Kickstart specific content types things could get really crazy. You've been warned. Go slowly.

I know you want to know how to do it in drush, but using the UI will likely be easier given the amount of time it will take to do this:


Uninstall the Kickstart specific modules. These will be all of the modules whose Package is Commerce Kickstart. There should be 18 of these. Disable one or two at a time. You have to do these first.
Once those are done, then you'll need to go through and disable all of the Commerce Contrib modules. These would be modules found under Commerce (Contrib), Commerce (whatever), etc.
Once those are done, then you should be able to disable the Commerce core modules.