Hi,
I have not faced "Whitelisting Policy" not working with Meraki Wireless.
I did faced Group Policy issues in Meraki Wireless + Appliance network which was shorted out later.
I never got an opportunity to Manage 1000+ WiFi user base though.
If not ISE / MS you may consider FreeRadius / MikroTik.
You may start with http://www.freeradius.net/. Install it on a Windows Machine and check if a Radius solves the issue.
However Lets wait for some more suggestion from Community Members.
Regards,
Ajit
AjitsNW@gmail.com
www.ajit.network