I'm thinking Pr is right. Something affected Preus so he wasn't a typical kryptonian anymore. But MM was surprised that he got hit (he believed even Superman shouldn't be able to hit him in phased state). I could be wrong though
Martian Manhunter is one of the few DC heroes that has quite a few unambiguous portrayals where the writer thought he was more powerful than Superman. On the other hand, there are even more portrayals where Superman is clearly more potent than MM.
So on the whole, Superman has the advantage.
The entire realism argument that MM SHOULD be more powerful than Superman is actually somewhat illogical. Basically, the fallacy is that you stop at an arbitrary level of realism but don't start really pushing realism as far as it might go. What about Superman's speed edge? Realistically, that would probably win it. Then again, the real issue with the realism arguments is that powers are never defined well enough to actually take realism to it's limits. How much faster is Superman than MM? Can HV affect an intangible MM? What is Superman's "realistic" resistance to TP? None of this is known definitively enough to allow for a fully realistic power set on power set evaluation.
So I tend to just try to get a feel for which character was rated ahead of the other more often and more frequently. The record is rarely 100% for either side, but there are trends. And overall, Superman is rated ahead of MM more often than not.