Only deactivating user profile can prevent a user from hosting a meeting and hence consuming the license. You are correct that if you deactivate a user, it won't auto-complete when scheduling via WebEx site. There is no other way to do this.
Still, scheduling meetings in Outook using PT integration can work around the issue with auto-completion of invitees with no active profile on CWMS.
I hope this helps.
-Dejan