We cannot use GPO to deploy "Log on As a Service" User Assigment Rights because it will modify and overwrite the membership of users or groups. But, we don't want to do that, we just want to add new user without affecting other users or groups.
The solution for this issue is to use Ntrights.exe from Windows Resource Kit.
The right command to add the user or group to "Log on As a Service" is:
ntrights.exe -u user@domain +r SeServiceLogonRight
You can deploy this command with your SCCM and you should include ntrights into the package.