PowerShell script that should find disabled users that are not in a specific OU outputs users from that OU as well

This sample batch file will do what you're asking. You'll need to edit the dsquery command to use your specific StartNode OU -- The OU=SomeOU,DC=example,DC=com bit:

@ECHO OFF
REM Get list of disabled users in the domain
FOR /F "usebackq delims=;" %%A IN (`dsquery user "OU=SomeOU,DC=example,DC=com" -disabled -limit 0`) DO ( 
    echo User: %%A
    REM Enumerate user's group memberOf, exclude "Domain Users" group
    FOR /F "usebackq delims=;" %%B IN (`dsget user %%A -memberof ^| find /V "Domain Users"`) DO (
        ECHO Group: %%B
        REM Remove user %%A from Group %%B
        dsmod group %%B -rmmbr %%A
    )
)

Something like this:

Get-ADUser -Filter * -SearchBase "ou=TheOU,dc=contoso,dc=com" | Disable-ADAccount

You might need to upgrade your Powershell version if it doesn't have the commands.

Try/Catch example:

$users = Get-ADUser -Filter * -SearchBase "ou=TheOU,dc=contoso,dc=com"    

ForEach ($user in $users) {
    Try {
        Disable-Account
    }
    Catch {
        Write-Output "$($user) is already disabled."
    }
    Finally {
        # Cleanup tasks, etc.
    }
}