If Congress were to pass such a law as you suggest, it would get struck down on challenge based on the Constitutional separation of powers. I would think that would be an easy challenge as it is so basic to the framework of the Constitution.

First, as we've seen time and time again, it's not always that easy procedurally to get a quick and decisive determination on Constitutional questions. Will the Court regard this as not a "case or controversy," but more a political dispute between branches? Will they determine that no cause of action exists until the criminal charges are filed? Many Presidential pardons are issued as the President is on their way out the door at the end of their last term in office - what if Congress passes this bill in December, and there just isn't time to get a final ruling before the President has to decide?

Secondly, I chose that example specifically to be an easy and obvious instance of Congressional overreach. But there are other, far more disputed areas that Congress could get involved. For example, the War Powers Act. For decades, the Executive and Congress have disputed the extent to which the President can conduct various military operations without a formal declaration of war by Congress. That conflict pits the Executive power as Commander in Chief against the Legislative power of Congress to declare war.

So what if Congress amends the War Powers Act to provide that it's a felony to violate it? Suddenly the calculus changes immensely. Now even if the President has solid (though disputed) genuine Constitutional arguments to support the scope of his authority to defend the country independently of Congress, he's facing possible - even probable - threats to his personal liberty over a Constitutional dispute between branches of government. The type of dispute that happens all the time in government (I can't remember if there's ever been a modern President that didn't lose at least one Constitutional case over the scope of his powers), but now Congress can force the President to hedge his bets by imposing the risk of criminal charges on him?