Yes.
The normal method would be to place all your workstations in a single OU and
apply the policy there. I'm guessing that all your computers (both servers
and workstations) are still in the default "Computers" container and that,
because you can't apply a GPO to this container because it's not an OU,
you're applying the GPO at the root of the domain.
So, just create another OU, place your workstations in it and link the GPO
at this point instead of where you're currently linking it.
Hope this helps
Oli