Unfortunately the only way these counters can be cleared is by reloading the router.
The reason for this is most of the stats are not directly accessible, they are displayed by making registry calls to the various active and registered protocols, so there would have to be an additional registry to clear the stats, and it would have to be added to all the protocols that register (probe, udp, ipmulticast, egp, igrp, eigrp, ospf, and tcp) as well as to icmp and ip itself.
Several DDTs (bug/new feature requests) have been submitted for this function, but were closed because of the complexity of the IOS changes needed.
