According to the base rules, a site used for pagan worship gained 1 point of magical aura per century. Before the rise of Christianity multiple sites would have been used for over 500 years, and would have had a magic aura of 5.
It is known that the Catholic church tended to re-use the sites of ancient pagan temples, reconsecrating them to Christian purpose. By the rules the divine aura would have started at 3 when consecrated (twice), and then have risen to 4 with a year of use, and to 5 in a decade *if* the site of the church is one of great significance.
For those that would not, however, this would leave a magic aura of 5 with a divine aura of 4, which does not seem to be the intent of the setting. Without a stronger divine aura the magic aura would not falter, and would leave an area where the magi aura dominates in the center of a great many churches.
The strengths of Divine auras aren't fully consistent throughout the books, but Realms of Power: The Divine suggests that the divine aura is 5 at the altar of even a small church:
Realms of Power: The Divine page 10:
Dominion power within a given area will vary. Inside a small church, for example, it has its strongest aura rating of 5 at the altar. This will decrease to 4 throughout the church, extending to the threshold of the church building, with the land and cemetery surrounding the church having a Dominion aura of 3. Within large churches or places of worship there may be several areas with high and low aura ratings, such as in the Church of Holy Wisdom in Constantinople — the largest church in Christendom — where the many altars, relics, and icons result in the Dominion varying between five and, in the holiest places within this holy place, 10.
The fact that the strength 5 aura is only one relatively small part of the overall aura shouldn't be enough to stop it counting for aura weakening given that RoP: Magic (pg 11) suggests that just brushing up against a neighbouring aura is sufficient. I'd also count Divine 5 as being strong than Magic 5 given it supersedes it when both are in place, so you're meeting the criterion for the -6 penalty to the magic aura stengthening / weakening roll in the table on page 10 for "Stronger foreign Divine aura impinges on aura".
I’m looking at p. 12 “after a decade a dominion aura may grow to 5 if the congregation is large, and the church is a significant one with wide importance”
If the aura is always 5 at the altar I would expect that to be stated (or stated when it reaches that point) rather than to simply look at one example and go “oh, well that’s why” as if that were all cases when it is not supported by the actual rules.
If there is always an aura of 5 at the altar that would address the issue fairly significantly (there would still be questions of how the magic aura is actually suppressed, which connect more to RoP:M than divine), but that isn’t really stated to be the case.
I think page 12 is talking about the main body of the church. The two quotes are broadly consistent if you assume you're talking about a small church that's been around for more than a year - the main body of the church will have a Dominion Aura of 4, which is what one cares about for most purposes, but page 10 says that at the altar the aura will be 5.
Exactly what the situation is at the altar in the first year isn't entirely clear (does it start at 3, 4, or 5?), but it probably doesn't matter that much - it will take time for the magical aura to weaken enough than the strength 4 aura in the rest of the church subsumes it anyway.
I think we can generally say that the Divine has supremacy over other auras. Cases are probably particular to the site and calendar.
Example: Major pagan former temple, consecrated by Church: The Magic* aura is generally subsumed, and declined as it’s not being maintained. The Magic aura is focused on the site of the idol, the divine aura on the altar. In general, the Divine aura reigns, but less so at night. On some pagan festival days the aura surges.
This could lead to some odd flavor mixes, some complementary, some contrasting, some clashing.
*I’m confused why the temples don’t have Faerie auras?
Part of it is that the concept of what was faerie and what was magic changed from when the basic book was published and later when the faerie book and others were published. Originally gods were assumed to be magic while faeries were gnomes and pixies and stuff.
However when it comes to the strength of auras that doesn’t really matter, because magic auras are established (when they are not naturally occurring) by repeated rituals, where faerie auras are established, for the most part, by the presence of a faerie- so the faerie god might have occupied the site originally, but human activity in the practice of worship could establish a magic aura.
As to the supremacy of the Divine, this is stated and consistent between books and reflects what is stated in RoP:D, that when auras are equal the divine will prevail, but other auras will prevail when they are stronger- it gives an example of a church with a level 5 divine aura which dives way to a faerie aura of 5 at night when teh divine aura weakens by 1.
Honestly I don’t think any of the authors ever considered how many churches were built on sites that would have been level 5 magic auras, because with that added in even a level 5 dominion aura won’t overcome a level 5 magic aura since it wouldn’t be consistent when it drops by 1 every night.