That made Olympus Descending extremely jarring. I would've expected that of New Frontiers, not of the DS9 relaunch.
Well, just because one faith system turns out to have an empyrical basis doesn't mean all will (in fact, considering the exclusionary claims that often come with these belief systems, it would be impossible for all to be correct as writ). But to give Olympus Descending its due, it does reveal that the Founder's faith was not pure invention but based in reality, since their deity does, in fact, show up, much of the same way Sisko et al. have run into the deities of the Bajoran faith, and found that system to have a tangible basis in fact. Of course, whether you consider the death of the Progenitor to put the Founder's belief system to lie depends on one's conception of what it means to be a deity. Many human cultures had deities who were mortal, who could and were killed. The Norse gods are probably the most popular example, but there are many more examples of the God Who Died trope. Of course, many of these then have a rebirth (Osiris, Tammuz, Adonis, Christ, etc.); and although not necessary to establish its divinity, for all we know the Progenitor is waiting to go all phoenix on us.
Fictitiously yours, Trent Roman