The Quiet Council.
Yes, Orchis and other Mutant hating groups/robots are a more overt threat... but they are like seasons. They come, they go, but make no mistake they will inevitably change and be replaced by another.
The Quiet Council however? They're a different sort of beast. a deep rooted one
If Krakoa is a Great Wood, then its leadership is a rot that does nothing more than seek to eat it from the inside out.
If anything can be gleaned from Inferno and the rest of the books, it is that Our Leaders can not be trusted.
They are petty
They are spiteful
They are Self serving
They are egotistical
And don't get me wrong, I fully believe they fully believe they have Krakoa's best interest at heart.