I think it was more intended as a check for "justice". Where someone could technically be guilty of a crime, but the conviction was considered unjust. You wouldn't necessarily want to repeal the law, but instead use the pardon to fix "edge cases".
There's at least 3 steps of bureaucracy between the president and the prosecution: Junior prosecutors->US Attorney->Attorney General->President.
He may ultimately be in charge of the prosecutions, but for him to take that much control is considered unseemly. The closest the President will generally come to deciding whether to prosecute someone is to make a policy that certain crimes will get extra attention or no attention. Alternatively, he can fire the US Attorney.
But aren't prosecutions done by the DoJ, as part of the executive branch, i.e. the decision to prosecute someone at all, or whether to offer a plea deal is already under the president's control?