I would like to prevent a player from entering a zone by setting a permission on that zone to allow everyone but that player. Is that a way to do this?

As far as I can tell, there is no way to blacklist players yet from entering a zone. Only a way to only allow players with a specific permission to enter a zone. I granted the default role that permission and tried revoking it from that specific player, which does not work since they are in a group that inherited all of the default role's permissions.

I would rather not have to create a whole new role for that specific player as the role he's in and the default role has a lot of permissions i would rather not take away from that player, and I do not want to prevent new players from entering that zone if I was to 'o.grant user * zonemanager.<custom permission> ' instead of 'o.grant role default zonemanager.<custom permission>'.

The only sensible way to handle this at the moment would be to have a permission that negates the other; which the plugin you are using would have to provide. There is no way to not inherit an inherited permission in Oxide natively.