There is already a mole on Krakoa- the one who killed the assassin so technically whoever he works for he is the first as he wants Krakoa to fall.The next suspect though it is for self interest purely not Krakoa's demise is Sebastian Shaw, Mystique after the last volume will definitely betray Krakoa,but only because she is being betrayed first.Sinister should have treachery tattooed on his forehead.
Regardless of villains, I would like to see Exodus lead a team. Sinister or Mystique seem the apparent betrayers. But the greatest threat to Krakoa will be the humans.
I put Mystique because that is so typical of her character.
Edit: Lol, she is winning. This would be something radically different in this hip new direction.
OP Question -
All things considered, Mr. Sinister or maybe Mystique, IMO.
"So you've come to the end now alive but dead inside."