Is Oedipus punished for his pride or because he killed his father and married his mother?
This is a bit of a "which came first, the chicken or the egg" question, only this one seems answerable. Let's put it this way, if he hadn't had too much pride and tried to outmaneuver the prophecies of the oracle, Oedipus would not have done either of those things--kill his father or marry his mother.
It's true Oedipus did nothing wrong to end up with Polybus and Merope; but once he deliberately tries to thwart the predictions, he must take responsibility for what happens.
It's true his father must take some responsibility for his own death--theirs is a battle of the wills which, ironically, shows their family resemblance--but Oedipus is responsible for his own actions. It's unlikely the gods are punishing him for the murder, when it's his pride which put him in this position. The marriage to his mother also occurs after the prideful running away Oedipus does.
If anything, then, the murder and the marriage might be punishments for his contempt of their prophecies.