If you look at the rule pzSystemMainMenu, you will see that the entire "Database" category is controlled by the when rule pyHasAccessToMTRestrictedRules. If you don't mind removing this entire choice (which looks like this):
You can change one of the privileges associated with the checks in the When rule so that the "Database" option does not appear at all.
There is no When condition associated with the "Modify Schema" option, however. I don't know if a request for a hotfix or enhancement would be considered. I also don't know if you wish to change your entire Portal, making copies of these two navigation rules so that you could have your own version of pzSystemMainMenu which in turn contains a visibility condition to control just this one option.