Try this work around
1. Create the exclusions for Autoprotect that you need.
2. Create a mount point for the excluded folders that you want to scan. (Map a network drive for example).
3. Scan the mount point (Network Drive) and because the system reads it as the mount point (network drive) instead of the actual location the exclusion wont happen.
Ref:
A suggestion for a work-around.
In the antivirus and antispyware policy under file system auto protect remove network,
create a separate scan for your mapped drive..
Note:mapping and configuring a new scan you have to do in the client PC and rest in SEPM.