While it does invoke certain supernatural elements I would disagree that this makes them less rational. Angels exist, but are fallible, mortal and material creatures composed of Dust. Dust itself is a fundamental particle with known and predictable behaviors, though admittedly ones that are somewhat implausible. The biggest leap is the world of the dead in the final book, but I found it a very good description of how awful an afterlife would actually be, and the problems with an all powerful god figure.

In terms of rationalist virtues, the children succeed by being self reliant and intelligent, and it avoids the heavy handed morality of most YA fiction (for example the main character is a skilled liar, and thats seen as a good thing when used well).