> Ordering violence orchestrated by the military is a core constitutional power. It's called being "commander-in-chief" of the armed forces.
Incorrect. The commander in chief, same as all military officers, has the authority to issue lawful orders to the chain of command below him. He does not have the authority to issue unlawful orders, and if he does, his subordinates have the legal obligation to disobey them. The president does not have constitutional power to order arbitrary violence.
> If Trump has a fight with Melania, he can order the CIA to rendition and disappear her
No he can't because this is against the law, and it is therefore not a presidential power. The president has no constitutional authority to order agencies to violate the law.
> He can then pardon everyone involved, so even the underlings face no court.
This is, unfortunately, true. But it has been true as long as the US has existed.
> If Trump receives a bribe, the official act that he undertook at the briber's behest is similarly inadmissible.
This is true, but the act of taking the bribe is not an exercise of presidential power so he can be charged with accepting a bribe. This is not new to the recent SC decision.