Ilya,
yes, as far as I know you can configure the NAC portal to perform user authentication against an AD (LDAP). Once the user authenticated, you should see the username and IP address within the NAC end-system list and the user should be in ACCEPT state - is that the case?
If so, then the Connect Fortigate integration will forward that data to the Fortigate. No matter where the username is coming from (AD, 1X, portal, etc.). Give it a try and let me know how it goes.
Kurt