Problem Solved

Jim Henley has the solution I’ve been looking for. Let the president keep the power to pardon, but:

Amend the President’s pardon and commutation power to exclude executive-branch employees convicted of crimes carried out in the course of their professional duties. Vest the power to pardon those people in the Congress, maybe by a super-majority of the Senate — a kind of inverse impeachment.

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Sounds right to me.