It would affect proggresion. In fact dramaticly because they would have to change the spawn requirments for a whole lot of bosses
Kill WoF = World changes to Hardmode, the V spread happens.
Kill Ferryman = World changes to Hardmode, V spread happens.
Literally the same thing.
Codewise, the WoF is coded to trigger the Hardmode transition and the V-spread upon death, if the world is not Hardmode already. It's a simple action that you call with the code, like
or something like that. This bit of code could easily be placed in the Ferryman too, the exact same way. In fact, you could stick this code in the freaking Eye of Cthulhu if you wanted, and it would act exactly the same way.
EDIT: Also consider this: Breaking Shadow Orbs calls code that enables meteorites and goblin army spawns. When they added the Crimson Hearts, all they had to do was have the Crimson Hearts call this same code, because the same thing happens when you break a Crimson Heart.
EDIT2: As to coding its AI, IMO, use similar AI that the Pirate Ship uses, and instead of dropping pirates off, it would instead drop ghosts off and perhaps instead of cannon balls, I dunno, have it showing spirit fireballs or something at the player.