So sorry to hear that some of your flock is ill. Very responsible of you to put them down so it doesn't spread. I believe they are safe for consumption otherwise I would think it would be a required test for the NPIP process in all states. Though Im not 100% so I hope someone else has an answer for you.
MG is not part of NPIP unless you pay for it. NIPIP is different in each state though.
If a flock has special or rare breeds, you can collect eggs and run the incubator at 104 for three days. That will kill the virus but reduce hatch rates by about 30%. The chicks will be MG free though. You would then need to brood them inside away from the contaminated area to allow it to die at your place before putting the chicks out.