I think that airplane will be considered captured by terrorists. If there's a danger of it being used as a weapon of mass destruction, it'll be blowed up to prevent more deaths. I don't think that it would be considered reasonable to blow up aircraft if it didn't present a danger to big cities.

So IMO pilot could ignore their requirements and I think that nothing would happen outside of angry transmissions. Especially if the plane was near border. But I don't think that it would be reasonable, especially in an airplane full of innocent people.