There's no question that Fallon's comments as reported in the Esquire magazine article put him in a tenous position. Bush, for better or worse, (I know it's worse) is the Commander in Chief and Fallon was clearly chafing against the limits of what is allowable dissent by a subordinate officer.
On the other hand, Fallon was performing a useful and patriotic role to the extent he saved the U.S. from a strategic blunder of an Iran war.
The question is whether or not this means there will a war with Iran after all. It's very worrisome if this clears the way for a war.