I recently felt like playing some FO3 after not playing it for a long period of time. I wanted to play it without FWE, so I deactivated its .esm and all if its .esps. I started playing, and I'm still getting features from FWE. For example, it asked me if I wanted the Vault 101 beginning or the alternate one, and when I picked the Bobblehead up off of Dad's desk, it only gave me 5 points rather than 10.

Is there anything special I need to do to make FWE stop?

You still have a plugin checked that has an FWE plugin as a master, like a FOIP or something. Even if the master is unchecked in FOMM, it will load if it is in the data directory and another plugin requires it. Don't delete the master - you will just end up with a CTD. Just highlight all your plugins in FOMM to see what masters they require.