Best way to manage users?

I'm having some challenges managing my users for PhishThreat. Since PhishThreat syncs users that are in the Disabled Users group (as far as I know it's best practices to disable rather than delete users) my numbers aren't accurate. Using AD sync I'm wasting licenses on users that don't work here any more. I was also told by support that during setup you're able to choose which groups are synced from but now that setup is complete I can't make any changes.

So how do you all make sure you're only including active mailboxes in your PhishThreat campaigns?