As for the case you cited, it was a civil suit, therefore ruling only covers civil law, not criminal. That said, does not protect "the plainly incompetent or those who knowingly violate the law". [1]
All Presidents are fully aware by law their powers are limited, no reasonable official would claim otherwise. No reasonable person or official would claim their actions were legal, hence why they knowingly hid them from FISA & Congress.
[1] Malley v. Briggs, 475 U.S. 335, 341 (1986).
The President does not have the power to fire federal prosecutors serving in subsequent administrations. It's true that you've provided the explanation for why (even without the DoJ opinion which currently prohibits filing charges against a sitting President) it is dubious that a President could effectively be held criminally accountable while in office.
After he leaves office, his only protection is relying on political concerns, or an anticipatory pardon.