Psion, it's a marketing stunt, that's all. There is nothing offensive in the BoED that is more offensive than the Monster Manual.
By your logic, they should have put a WARNING! on the MM. It does contain racy pictures. Hell, it deals with Demons and Devils. Demons and Devils are more offending to religious folks than Stygmata.
Dealing with religious issues is not a matter of maturity, it's a matter of personal values. Religious content might offend a 60 year old, while being O.K. to a 12 year old (I do not think that it will offend anyone, but I'm humoring you for argument sake). Note that the book doesn't promote a religion over another. It has a christian bent, but nowhere does it promote it against other religions.
Nudity, on the other hand, WILL have an effect on a 12 year old. As will profanity, and violence. Which is why warnings are issued on such products.
If they wanted to advise people about the religious content, they should have written :" Contains material dealing with religious issues ".
No, instead they put:
WARNING!
Content is
intended
for mature
audiences only.
That, my friend, is nothing but a big tease.