I agree everyone, including the President, should have checks and balances, but on the other hand there is the need to act with rapidity (and perhaps mystery and violence) in certain unfortunate and hopefully rare circumstances.
So, how about we have a special court, like the FISA wiretap court, that could authorize “unlimited” treatment? The President could apply to this court, in certain very rare circumstances, for approval to treat a particular person in any means deemed necessary by the President. The target individual would have to be named.
The law would be written so that this could not be applied to any U.S. citizen, nor against anyone to whom the Geneva conventions apply.
The members of this court themselves would be subject to sanction (up to for example charged with homicide) if the Supreme Court found that they were discharging their duties improperly.
To further limit abuse, perhaps the members of this court could be chosen randomly from among appeals court judges, and perhaps they couldn’t serve for very long, like for say 1 year.
This would give a legal mechanism to treat some folks badly, when necessary, and to put fear into others of what might actually be doable to them.
Perhaps the court would be required to release the names of the folks so declared or perhaps the number of folks so declared each year.
You could write into the law that the President could be held liable for inappropriate declaration, and that this would not be pardonable by a subsequent President.