Kino and Juana funtion more or less on a primitve level in their lives and in their religion, yet they both want a church wedding and a christening for Coyotito.

This has very much to do with the influx of catholicism in their community. Missionaries come with ideas that permeate the indigenous culture. KIno and others often mix Christian theology with their own beliefs. Kino has his baby baptized, perhaps, out of a sense of guilt. There is also the fact that the church helped those people, financially, who practiced. I don't think they saw it as a contradiction in the same way that we see it.