As you may very well know AX can't be deployed with other directory servers than Active Directory (AD). But a product like Microsoft Identity Integration Server (MIIS) allows you to integrate between AD and other directory servers. This will allow you to use AD only for AX while continuing to use another directory server for all other purposes. You can find more details about MIIS at http://www.microsoft.com/technet/miis/default.mspx.
This posting is provided "AS IS" with no warranties, and confers no rights.