Gov. Walker does NOT have the power to fire municipal clerks. That is up to the individual towns, villages, and cities. IOW, that is up to YOU. If citizens of Wisconsin put enough pressure on their Aldermen and other Representatives, the inefficient clerks will be replaced.
One thing the state CAN do, is pass a law such that if the military absentee ballots from a district are not mailed out on time, then NO absentee ballots can be counted from that district.