IMHO, if they sincerely questioned the legitimacy of Bush's presidency, they had the duty to question orders until either a. his legitimacy was demonstrated to their satisfaction or b. they accepted the consequences of disobeying lawful orders c. they resigned.
“c. they resigned”
And that is about the only way an officer is going to be able to refuse the orders of the President.
Think of the common sense argument here: If the Supreme Court, Congress, and the military Chiefs of Staff recognize Obama as the ligitimate President, what chance does a Major have in refusing his orders?