It's traditional, having its roots in the divine right of Kings. Governors have the same power wrt state offences.
Yeh, sure, it can be misused for political purposes, but it's a necessary and desirable part of the executive toolkit. If anything, few executives use it as frequently as they should for fear of political backlash from the law&order vengeance crowd...
Dunno who said it first, but the idea that "a society can best be judged by the quality of its mercy" would seem to apply...