I think you should kill the bees first (with soapy water the evening before)
From the MAAREC website-
Control: Sanitation and elimination of disease reservoirs
is a necessity for adequate control of American
foulbrood. The traditional control measure is to
kill all bees in an affected colony and then destroy
bees and their comb by burning. The hive bodies, bottom
board and covers can be salvaged by scraping thoroughly
and then charring the inside portions and/or
boiling in a lye solution.
Hope you get out of it with the least damage
There is no greater satisfaction than the satisfaction of a job well done.