If you'll spend a few minutes actually reading the FairTax bill (several links given on this thread but if you need one, just ask) you will see that there is none of the "earmarking" you describe outside of the S/S & M/C programs (which funding is required by existing laws).
For a state to adopt a FairTax-conforming sales tax, that state system would also have to have no "earmarking". If your state has a real problem with that at present, you should begin hammering on your state folks to adopt a FairTax-conforming law when the FairTax is passed. If you'd start talking that up now, you'd have a headstart on most states and would help get your state ahead of the game.
In one particular state, I have had discussions with a prominent state Senator about doing exactly that.
Great point.