It's not the "worst thing ever" but it is bringing the game into disrepute etc. Elbowing someone on the pitch is not "the worst thing ever". Fielding an ineligible player is not "the worst thing ever". It doen't need to be for the FA to dish out a sanction.
He is going to be punished by the FA as an individual, just depends on the level of time / fine etc.
It is nothing to do with Steve Gibson or Middlesbrough now. Just need to accept we got caught doing something stupid.