The roll pin is probably for the hand crank. Clean it up and lube it and it should come out easily with a punch and hammer. Wisconsin flywheels typically come off very easily. Use a soft hammer on the crankshaft so you don't mushroom the end of it.
The aged parent welded a pair of 'vise-grips' to a pipe plug that fit our slide hammer for pulling spindles on a cotton picker. Something on that order should work if the vise-grips alone won't. That's a new locking arrangement to me, but I'm woefully short on Wisconsin experience.
I really do not think that pin was put in at the factory. I have worked on several of the Wisconsin twins and I have never seen one with a pin there. I have seen some with a split nut and an Allen screw in them to keep the nut tight. That was on an engine used on a NH 66 baler when they first came out.
That looks like a home made setup to me. Think I'd try running a self tapping screw into the roll pin and put a small prybar under the head of the screw and on the end of the crank for leverage. Pull it out like a nail. First thing would be plenty of soaking with penetrating oil.
If this doesn't do the job then a small grinder to cut it off flush with the flywheel would work.
The way it looks, the pin is not holding anything anyway. It looks to be on the wrong side of the flat part of the nut to do any good (wrong side of center). If it moves a little in with the hammer, it will most likely pull out easily.
I cut the pin with a die grinder and got the nut off.
I showed the engine to a guy who knows Wisconsin engines pretty well. He said that the rope starter/ v groove pulley was not original to that engine and that the roll pin was put in there as a drive pin.