Originally Posted by The Question
The entire point of that episode was that Superman was letting his distrust of Lex Luthor turn him into a paranoid dick, and he was taking out his frustration on Captain Marvel because Marvel reminded him of himself before he got all jaded and paranoid. The level of destruction in that fight was meant to paint Superman in a negative light as a continuation of that theme. It has everything to do with the damage done in the fight, and it's the big difference between the fight in that episode and the fight in the movie.
I seem to recall that the whole season the villains had manipulating the Justice League into looking bad and this was one of the final straws.