There's maybe one President that didn't get elected because of his use of the pardon. But then, Ford wasn't elected President or Vice President before he pardoned Nixon either.
Otherwise, I'm not aware of a pardon so controversial that it became a major campaign issue. And for a second term President, there's not really any downside.
Because the pattern they usually follow is to pardon the questionable cases (personal friends, people with financial ties to the President, etc.) just before they go out of office.
If America mistrusts government so much that it wants the President to be a de facto monarch, it should just drop the pretense at being a republic and have a monarchy already. Or make the oligarchy official and elect a CEO in chief. At least then there's only one head for the CIA to put a bullet into.