We do this.
We have Moodle authenticate against an OpenLDAP Server, which in turn acts as a proxy to merge two separate active directories in to a single LDAP view. This is done using openldap's database meta backends to dynamically connect to each different AD in real-time. Moodle (and any other LDAP aware apps) are then none the wiser that multiple Active Directories are being queried as we re-write it all in to a single/different LDAP tree / view.