Yes I can see that reading! It's partly because the framing sequence has to endlessly postpone Sandoz's catharsis until the denouement.

I had trouble with the atheist character coming to terms with God by hating him (what's wrong with simply not believing in him?) leaving everyone in the book a believer, but that's probably my own baggage.

I also have trouble deciding whether the book shares the views expressed in the closing pages, that the most horrendous indifference and suffering only means we must redouble our attempts to understand God's will. It would be quite easy to read the whole book as pulling the rug from that argument, except that it uses it as its summing up.