If you think that a gay pride flag isn't a political statement, then I assume you also think a white pride flag isn't a political statement?
Edit: Also, if the inclusion of a gay pride flag isn't a political statement, then how can its removal be a political statement?
The fact that it's a political statement you and I may happen to agree with doesn't mean it's not political, and advancing that argument just makes you sound as irrationally prejudiced as the people you oppose.
The article says that the target of the complaint wasn't even told about it, so how can she possibly have been "fucked over" or "traumatized" by it?