The present-day Unitarian Universalist Church is well known for wearing its politics on its sleeve; it's left-wing, loud and proud. Combined with the political content of the scene, and recent Trek's unsubtle attempt to make thematic commentary on present-day American politics (see Paths of Disharmony), I find Mr. Mack's characterization attempt unsubtle, overreaching and out of place in Trek.
The funeral occurred in a Unitarian church, yes That's the only content referencing the denomination: all of the thoroughly secular dialogue in that scene was delivered by President Bacco.
I don't know why people choose to take offense from the mentioned existence of something harmless that they dislike for whatever reason. Is difference that frightening?
Were people this upset with the Bajorans & the Prophets? I know theirs isn't a real religion (sorry to break that news) but I see no difference to a scene at the Bajoran Temple on DS9 & or one at a Unitarian Church. It isn't some subtle attempt to offend anyone, just a scene that gives a broader look into people of the 24th century.