That is not a problem because those guys ARE intended to be broken no matter where they are in. It is a normal occurrence in any pokemon game. It's player or official sanctions in 3ds games that prevent them from "ruining" the game.
If pvp has to be made, just restrict that only 1 legendary pokemon can be in a team in addition to one pokemon of each kind only.
EX Raids and Ridiculous flee rates are more of a problem than this.