Deploying AD to your SmarterMail server shouldn't cause any issues with your existing users. Once you have AD configured on the server, you can then switch your users over from SmarterMail authentication to Active Directory authentication.
To ensure you don't run into any port conflicts, you may need to instruct SmarterMail to not listen on the LDAP port. To do this navigate to Settings -> Bindings -> IP Addresses. Here, you'll need to edit any IP address in use and verify that the LDAP port is not checked.
I hope this helps.
Technical Support Supervisor