Hadn't heard of this book, I'll have to check it out. It vaguely reminds of something Dostoevsky's Underground Man might have said when he was railing against the utopian rationalists.
edit: typo
edit: typo
It does help if you have some knowledge of the ways of the Catholic Church when reading the novel. I don't think I could have fully appreciated the richness of "Canticle" if I'd read it at a younger age when I'd had no experience with the Church. But I'll also say that it's one of those books that I love but don't reread too often since it always leaves such an impression.
But yes, I would say that the dangers of pure rationalism (without the wisdom to temper it) is something of a theme throughout "Canticle".