Been there, done that. :'(
I keep my plants in a plastic container, sort of like a laundry basket but with 1/4" holes so the fish wont' swim half way through and get stuck. Water can pass through, but the fish can't get in and wreck things. For some years, all was well with the plants. But eventually, the koi get big enough to do damage. The basket idea is new this year, and it's working GREAT.