Read the article: "Unlike the scouts, public officials are also bound by a line of Supreme Court opinions barring taxpayer support of any group that discriminates." Charging under fair market rent constitutes supporting the group that is discriminating. Charging fair market rent is not. So it sounds like the city legally can't cut the scouts any slack.
That statement is your own opinion and is not part of the article nor the Supreme Court opinion being referenced. The actual rate for "fair market value" is also not a part of the Supreme Court decision being referenced.
So again, it is not a legal issue, but an issue of whether or not the City "appears" to be "supporting" the Scouts by charging $1.00/year versus $200,000/year.
Because a reporter says it in a newspaper doesn't mean it's true; in fact, that may be a good indication that it's propaganda, and off the point of the legal priorities of the case involving a lease agreement that long, long predated any recent discrimination statutes.