[Know et al]

Question: What would happen if an officer now in Afgan./Iraq, were to file a suit such as the one Major Cook filed, would their orders be rescinded?

[pennboricua]

I am afraid that in that case as CIC obama would have him shot.

[mountainbunny]

Question: What would happen if an officer now in Afgan./Iraq, were to file a suit such as the one Major Cook filed, would their orders be rescinded?

Almost certainly not.

At the minimum, the officer would be charged with something related to refusing to follow orders, maybe Insubordination. No one is too big to avoid suffering the consequences of not following an order. See for example: Douglas MacArthur.

Followed by a Court Martial.

Followed by (if convicted) a trip to lovely Fort Leavenworth, Kansas or similar for many years, being discharged, or having your rank striped. Or all of the above.