If there are pass rules on LAN, then the traffic is going to get out of the source end. But if you really disabled all OpenVPN rules on the remote end, then the traffic must be dropped on arrival at the remote pfSense. That should stop any intranet-based Skype connection from being set-up, and Skype should end up finding its way out to public internet Skype servers to make the connection.
If you are just using the site-to-site OpenVPN for traffic to servers at other sites (like you say, using RDP, or file-shares or…) then you can make the rules on LAN to pass to just those remote server IPs and block to the rest of the remote intranet subnet/s. And similar rule/s on the OpenVPN incoming at the end for good measure. That should stop client-to-client stuff across the OpenVPN.