Wish Maker only meant an attack that ignored Bodies that affected the damage the attack deals. For example, Honchkrow Lv.X's Feint Attack (Let's pretend it CAN be affected by Weakness. I am way too lazy to find something that has Feint Attack, or a similar attack that is affected by Weakness, but not by Bodies.) It only ignores a Body if that body directly affects the damage being dealt. Meaning, if that Poke-Body is on the Pokemon you are attacking or something similar. The Body isn't directly affecting the damage you are dealing, it affects your opponents entire field by removing any weakness all Psychic Pokemon have. Weakness isn't an effect on the damage being dealt, it is a game mechanic.
Also, Feint Attack and other attacks like it do not prevent the Body from working. All they do is look and see if anything is affecting the damage you are dealing. For example, a Body that would be ignored is the Poke-Body of Abomasnow SF. It makes all damage dealt to any of their Pokemon be reduced by 20. It directly reduces damage dealt, removing the Weakness is not directly affecting the damage you are dealing.