That's pretty much entirely up to the FAA. They can, for instance, revoke the type and manufacturing certificates and Boeing doesn't get to make and sell aircraft anymore.
What likely happens? They don't let them sell until the problems are addressed to the FAAs satisfaction.
I'm pretty sure if the FAA revoked the type certificates the airlines would take out a hit contract on all administrators involved. (joking) That would burn more money than the GDP of most countries.
The FAA has authority to ground the entire fleet.
It probably won't go that far, but it does have the necessary authority to enforce a pretty huge "or else".
A more likely penalty is that they refuse to certify any newly manufactured plane.