I think it's great that he's patriotic and wants to fly his flag! As a former member of the US Army I totally get it. But you need to comply with local codes. Now if the flag pole were installed previously and was within the code standards it has to be "grandfathered" in, but it sounds like when it was installed it was already in violation of the code.
It sounds like he ought to try to work out a deal with them if it's truly a safety issue. Social media is a curse as much as blessing...
I used fly a flag outside my business years ago until it was stolen on two separate occasions. After that no more flag for thieves to steal!