I think a warning would be fine. Pokejobs are completely optional, aren't they? So there's no need to force people not to use them if they want to change the difficulty.
I have been really enjoying this hack, but I made an account just to say this. The idea of causing the game to intentionally crash when using Pokejobs just to "prevent an exploit" is utterly insane to me. Couldn't you have just recommended people not use the exploit? In a game where you can...