Maybe it depends on one's circumstances? An LDS sponsored club is not anything evil and I would join one if an independent alternative were not available. But some of the reasons I prefer my club to be non-affiliated with any particular dive shop are:
There are more than a dozen shops in my city, if each shop had their own club the dive community would be divided into factions. I believe a dive club should unite the dive community, to serve the interests of all divers regardless of their local (or online) shop preference.
As a non-profit, divers know our trips and events do not have a profit motivation. Any profits made are returned back to the members in other events such as the Xmas party.
Our club does not sell gear or classes therefore when we feature gear at our meetings it is purely to educate divers about that gear, not sell it. When we speak about training it is purely to better the skills of divers, not fill classes.
Dive shops come and go, look at how many have closed in the last few years. Dive clubs can last for as long as divers want them to.
Every member has the right to their opinion but as a club we do not sanction one shop over another, one manufacturer over another, or one agency over another.