Reduce the power. It's much more easily said than done obviously, but things like exemptions just should not be done. If the FAA makes a rule, it needs to be adhered to. The FAA needs a spine. Whatever we need to do in terms of reform to achieve that is up for debate, but we aren't even having that conversation yet.
In all seriousness though, what can be done? It appears that Boeing has to much power in their relationship with the FAA.