I've always looked sideways at a person in civilian clothes saluting a person in uniform. But the flipside is that, while a salute is certainly martial, the military doesn't "own" the gesture . . . and ultimately, that's all a salute is (if done by a civilian).
That's not the exact issue here. It's a Marine, in uniform, saluting a superior in civilian clothes. That's required. A return salute is quite different than Kerry saluting the Democratic convention. While perhaps not required, returns aren't, it's a mark of respect, in this context from the Commander in Chief to those serving the nation.
The author is way out of line.