Swapping clock and data is unlikely to cause damage, they are electrically identical signals (and quite safe - open collector), only their meaning is different.
What can cause permanent damage in some PS/2 hosts and/or devices is loss of ground connection, and that's a situation which may temporarily occur if you hotplug PS/2. Many devices are OK, but technically you are not supposed to do that.
Are you sure that thing doesn't require some drivers in Windows?