nah, the Action Replay (or any similar cartridge) alone won't help you win any game. If you are refering to entering cheat codes / altering hex values with the cartridge, well *that's* cheating because you alter the program itself. Using autofire doesn't modify anything in the software and is a whole different matter to me.
Your point is like saying "wheee, no, you can't use a joystick or even a steering wheel to play a racing game, because there may be some people who use the keyboard to play it, and that's harder, so they have a disadvantage". Well, they do, no doubt about it. But I never heard anyone demanding to plug off sticks and wheels just for people to get even...