One common theme when an author wishes to have a redemption arc for one of the series' more bigoted characters is to include some aspect(s) of paganism as part of a hypothetical magical culture. Under these scenarios, such culture is typically being repressed/suppressed by Dumbledore. His reasons vary with the work, only sometimes make sense, and are irrelevant currently. That is not what I am reacting to.
The more interesting thing is that these works almost always depict a fairly light and fluffy paganism. There are only occasionally gods/goddesses; it is more frequently some sort of almost pantheistic scenario, where magic itself is deified. There are two issues with this depiction.
The first is that it is far more likely, given the elements of Egyptian archaeology in the series, that powerful wizards and witches across history created the various pagan religions than that they believed in them. It is easy to picture Osiris as having undertaken one or more magical rituals to unnaturally prolong his life, possibly even horcruxes. The capriciousness, infidelity, and (bluntly) cross-fertility with humanity that the Greek and Roman gods display across their mythology becomes instantly explainable if the magical community there lived slightly apart from, but often interacted with, the non-magical community. These are just two easy examples.
One might respond that this is why the magical community does not seem to mention a specific god/goddess or set of gods in most works, but worships a vaguely sentient but ultimately generic ‘Lady Magic’. The problem, as I see it, is that having a family history of having been ‘gods’ should have made them cynical to the idea of religion. It should not require some 20th century suppression, it should have naturally faded away as the various magical communities simply became full of themselves and thus ignored any manifestations of sentience in the magic they use.
The second problem that this introduced religion is frequently just a vehicle to justify and/or ignore the inherent [immigration] problem that you set up the moment a bigot becomes even remotely ‘right’ or ‘good.’ Dumbledore aside, it cannot be the fault of those not born to magic that they do not know, when they are not exposed to the idea, that the magic they so casually use across Hogwarts is in fact a sentient force, almost a being.