I think it was a sort of hand-me-down from English law. But aside from that, each branch of government is supposed to have checks and balances from the other branches, and this gave the POTUS a bit of a check on the judiciary.
It was controversial though, and some Anti-Federalists (those were the group that opposed having a strong federal government and wanted most of the power vested in the states) opposed pardon power or proposed other versions of it in which the POTUS wouldn’t be able to pardon for offenses like treason, for example. Of course, that version didn’t end up in the Constitution and the pardon power a POTUS has is pretty broad.