How do I remove ALL ghosts BUT keep them in family trees?

@RoxxiRiott There is a bar night for ghosts that will cause them to all show up so you might want to have that turned off (it is a setting in MCCC).

Over on MCCC's webpage, there is actually this exact question with an answer.
"How do I keep my family tree Sims from being deleted when they become ghosts but still clean-up the other ghost around town?
This is very easy to do. You want to flag the Sims in your family tree with the “Never Cull” flag. Then, you can enable the MC Cleaner “Clean Ghosts” setting which will delete ghosts around town on a scheduled basis. It will not, however, delete any of the ghosts you flag for “Never Cull” and neither will EA’s culling, so it will always keep your family tree intact. If you can’t click on a ghost in the Relationship Panel to flag them, you can run the “mccc” or “flag_sim” console commands to do it. Those are documented further in the MC Command Center module documentation."