No, that's not a metaphor for some sort of weird relationship between Superman and The Joker! In the alternate Injustice: Gods Among Us universe, the villain found a way to drug the Man of Steel, fooling him into thinking that Lois Lane was Doomsday. However, The Joker came up with a convoluted scheme which meant that a nuclear bomb would destroy Metropolis as soon as Lois' heartbeat stopped (which it did when Superman killed her). Distraught by all this and the fact that Lois was revealed to be pregnant, Superman crashes to Earth and punches his arm through The Joker's chest, killing him in cold blood as a shocked Batman looks on. That was all part of the villain's plan to break Superman's mind. He succeeded, and in the Injustice: Gods Among Us video game, Superman became a tyrannical ruler on Earth who was a shadow of his former self.
