*pities the Jesuits for being expelled from Japan*
There is one called Paul of Tarsus (not sure how much NO bufoonry does it contain):
http://www.mangahero.com/manga/paul_tarsus_to_redemption/?manga/paul_tarsus_Also, Japan may have more liberal standards in media due to their naturalistic view of life.
But you should not generalize that all of them are perverted. Actually, Tokyo was taking steps to close the "cartoon loophole".
But, even if you find one that is chaste, there is a big chance of being packed with occultism due to the secularism and the predominancy of Eastern spirituality in Japan.
I found a manga called "My First Communion"
http://www.oriens.or.jp/shyoseki/b027_hajimete.html, but it's all-Japanese and its' style might not appeal to your son as it is more close to Western cartoons. And as again, it might be involved with the NO.
But your son might become a missionary to a land where half of the Catholics are sick of the NO.
Also:
http://www.womenofgrace.com/blog/?p=1089And for missionary activity:
http://www.traditio.com/comment/com0510.htmand AgnesRoma's posts.
Catholicism is often misrepresented in anime/manga, like, a nun is depicted hearing confessions. Actually, a lot of people have no idea what Catholicism is, they think it is "hip".
And take in account that this comes from a fan.