She's not mocking Chasuble: it's clear that he has the skills required of a clergyman. Rather it is a joke based on the idea that people who write books know nothing. From that, it follows that not having written a book is a sign of intelligence. It's a typically Wildean reversal of common sense. If she was being sarcastic, she would be implying that Chasuble is actually an idiot, but that doesn't match either her character or how Chasuble is otherwise presented.
The main characters are seeking a clergyman who is sufficiently skilled his day job to perform a christening, which Chasuble is apparently able to do (he boasts of his skill at this elsewhere and discusses the adequacy of sprinkling vs immersion). Cecily is praising him as up to the job. They don't require someone of particular book-learning or literary ability, just someone who perform the rite. Elsewhere we learn that Chasuble has a number of unpublished sermons and some classical knowledge, so he's not stupid but equally he's no genius.
Cecily is described as a character with common-sense and a good nature, not someone who would be cruel about Chasuble or mock him as insufficiently educated. For instance we're told she "has got a capital appetite, goes long walks, and pays no attention at all to her lessons." She also complains that studying German makes her look ugly. Her humorous remarks usually arise from a whimsical or superficial understanding of the world, rather than cruelty.
Despite her good nature, she does offer a less than flattering comment about novel-writing: "I believe that Memory is responsible for nearly all the three-volume novels that Mudie sends us." Even here the joke may be Wilde's rather than hers (for me, her remarks of Memory don't strike me as very in-character, sounding more like Wilde than an 18 year old girl). Throughout the play Miss Prism's literary endeavour ("a three-volume novel of more than usually revolting sentimentality") is mocked, so this fits with Wilde's disdain for the practice of writing books. Certainly we should not think less of someone who has not written a book.
The audience will probably regard Cecily's method of argument as both ridiculous and also perhaps with a kernel of truth, hence the joke. But it's not intended to be cruel or cutting by her. (Quotes from Project Gutenberg text.)