I think you are right to question that the book does not question the right-ness of the expedition being secret (as well as/more than religious). I mean, the characters can -- whatever the characters do, but this bit about how "The United Nations required years to come to a decision that the Society of Jesus reached in ten days" -- this long & cumbersome process of MULTILATERAL ACTION is what it is for reasons with which, I think, characters in the book would sympathize. Or at least for reasons of which they would be aware.