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.