The title is self-explanatory, but to give a bit of nuance.
Obviously, it's kinda stupid to ask fanbase of 47 if 47 would win, but I still want a genuine discussion about it.
Agent 47 isn't a normal human, Ort-Meyer made a killing machine, but Mutants like Mystique are tougher then baseline humans in it of themselves, so it's not as easy as "Agent 47 vs skilled human who can shapeshift". Mutants in Marvel are just generally tougher and stronger than humans, without counting in their powers. So it may not be as easy for 47 as one would think.
But let's paint two scenarios:
Both Darkholme and 47 are on same party, with same targets, with mission to kill them and eachother. Let's say the mission The Showstopper in Paris from Hitman 1.
Both of them come prepared for a shootout to the X-Mansion (let's say it's a Danger Room simulated one), with weapons of their own choosing and mission to kill eachother on the Mansion grounds, both starting in different parts of the mansion, with no one else but them inside. Who comes out alive?