You are correct. Flying the flag upside down is intended to be a request for help with an immediate physical danger, not a signal of political disgruntlement. You could think of it as the visual equivalent of calling 911. Call 911 to complain that you don’t like the current government and see what happens.
But you’ll never convince a lot of people of that. To all too many, it’s OK to disrespect the flag as long as you’re doing it from patriotic motives. The logic of that is hard to follow.
Referring to this event as no more than the result of a political disagreement and use of the American flag to send a distress signal as disrespectful seems both an enormous understatement and emotional overstatement.
How would you judge a platoon leader that calls an air strike on his overrun position? At what point should he make the call?