Ah, he meant those references to actual religions such as the Anglican Church, the Russian Orthodox Church and the Roman Catholic Church.
This series may not sound good in countries that say, have majority of people as adherents of Christianity, depending on the sect.
This could be a problem if the country you're talking about is a predominantly Roman Catholic one. Because ToAru depicts
the magical faction of the Roman Catholic Church (which I believe the Church has organized to fight against the "enemies of God" which can only be dealt with by occult means) as the antagonists, I am expecting devout Roman Catholics (and I mean the real devout ones) to protest vigorously on this one, when in fact the ToAruVerse is only
fiction, and does reflect the dark side of the Roman Catholic Church to some extent.
Recall The Da Vinci Code if you don't believe me.
I'm not sure how the real Anglican Church receive of this, but I don't think its devout believers won't receive it nicely, even though they are depicted as the protagonists, since it deals with magic, which is not actually a turn-on when talking about religion.
Judaism, for one, rejects the occult, and since all Christian religions actually have some ideas of Judaism within it, such as this rejection of the occult, naturally, a true devout Christian will definitely dismiss magic, white (Index and the Roman Catholic battle nuns) or black (Stiyl, Sherry, and Oriana) as the work of the Devil. Even if it's just fiction.
Fortunately, I think ToAru isn't flamed that much in Japan, since Christians are only a minority there, AFAIK.