It seems pretty clear at this point that if our current President had paid closer attention at school, he wouldn't be so confused about the difference between the "separation of church and state" and the "separation of powers." In other words, he'd know that they're not the same; that church and state refers to the difference between what people believe, a private matter, while the state is concerned with what people do in public.
He'd also understand that the separation of powers applies to the three parts of government: the one that makes laws; the one that carries them out; and the one that decides whether the first two have done their job. And if he understood that, then he'd be more concerned with carrying out the law, since that's his job, and leave law-making to the Congress. And he certainly wouldn't be wasting a lot of time and energy trying to get the judges to throw out the laws that the lawmakers have crafted, just because he happens not to like them.
Finally, if our current President understood the difference between a law-maker and a lawman, he'd realize that his complaints about John Kerry are totally misplaced. John Kerry has been a law-maker for a very long time and a lawman for only a little (as a state prosecutor in Massachusetts). Now Kerry's decided, very likely because our current President comes very close to being a law-breaker and has certainly done a poor job of carrying the law out, that he wants to do the job of putting laws into action himself.
So, in effect, John Kerry is saying "We can do better than that" and the President is saying "No you can't." To which all I can say is "You wanna bet?"