The fairest way would be just to award Hull a bye, and therefore announce them Play-Off winners.
The only reason the final is going ahead is due to how much money it makes for the EFL.
Re: The second point, every team in the division could make that point. Wrexham, for example, could make the argument that they should have been in the Play-Offs because Southampton had been cheating throughout the season.
I don't think it's disasterous that they've put Boro in the final in their place, it's not like it's made it a farce or anything, but I do feel for Hull - especially if they don't win.