"Centralising" a "decentral" design
I suggest creating a single common database. In this common database create your user table.

Instead of a login_has_site field, have a table of access that can be joined:


primary user id (of common table)
client name (other database)
user id in client db


After you have have that you can start to deprecate the fields in the user table across all but the common database's user table.