Earlier quoted context omitted.
That deals with immunity to civil liability, not immunity to criminal prosecution. There's no necessary relationship between them.
The president has the power to fire any federal prosecutor, there should be no expectation that any action he approves of will ever result in criminal prosecution. Civil liability is the only mechanism for holding those in the executive accountable besides impeachment. Many violations of rights are not criminally prosecutable anyways.
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.