I’ll preface this by saying that I’ve never read this book. However, it was assigned reading by the Spanish language program at my Catholic high school for many, many years. There were a lot of very orthodox teachers at my school, the principal was a priest, and well over 70% of the students took Spanish. And never once did I hear a peep about that book, other that occasional complaints from the students that it was long.
It is entirely possible that it does not portray the Church in the most favorable fashion. That is no reason why it should not be read. It is a classic piece of literature. You did not say how old you are, but my guess is that if you are old enough to be assigned this reading, then you are old enough to listen to opinions about the Church that are different from yours and not have your faith shaken at its roots.
I hope you enjoy the book.