Its outside of the intention of the rules
Nope. The rules don't have an intention other than helping people play a fun game.
turns the fun for everyone including me as the GM into a bit of a crawl
Maybe you don't find fun in it as a GM. What if the player does find fun in being smart and creative about beating opponents though?
There are those who play superheroes so they can go through crazy plots in a comicbook universe - and that is fine for them. There are also those who play superheroes so they can beat the villains by creatively using their superpowers and finally impose order in said comicbook universe so civilians can be safe from the crazy plots. And that is also fine - not everyone has the same preference and finds the same things fun.
as people try to add ex machina powers to Superman, rather then just have fun with it
Adding new powers is not the same as creatively using the existing powers. But both can be just as fun as only using the iconic powers - depending on the player's preference. And it is not as if the suggested effects (lobotomy, X-Ray brain fry) haven't actually being used in comics before.
#1: If you, as a GM, intend to limit the players in the way you believe the game is fun, then make sure they know what you consider fun in advance so they don't try for something that might ruin your fun or cause arguments.
#2: If you, as a player, intend to do something you consider fun but is potentially unusual, then make sure others know in advance so you don't ruin their fun or cause arguments.
(i.e. I've started asking GMs of games I apply to how much mobility, supersenses, and raw character power they are willing to allow before making an application and/or what is the scope of potential challenges so I know not to introduce things that might break their game)