If the uprooting is accidental whilst just grubbing around in the 'mud' a coating of pebbles might stop it. If they are pulling the plants up then other than placing a guard around the plants or putting them where the koi dont go I dont no of any other 'guaranteed' solutions, they could probably hammer even rooted oxygenators. You might try hornwort which is a 'floater'. I dont have koi so this is not a problem I encounter and some koi dont do this.
When you bag up the roots on the plants use a nylon netting the same as your mothers curtains, Then put a few rocks on top. If you pack the roots upside down & I use supermarket stainless steel baskets so I can separate them at the end of the season. They cant get into the nets and a layer of large stones will also deter them. Fish cant stop what comes naturally they will root all day Regards www.fishkeepingsupplies.com Aquarium and Fish Supply Tropical