No. Teaching materials that "transcend [the] scientific method" defeats the whole purpose of having a science class in the first place. For science, process is everything. If you're teaching kids ideas that aren't subject to standard methods of scientific testing then you're not messing with their ability to understand science.
You make it sound as if the whole purpose of having a science class is to brainwash kids into believing that there is no reality outside of what can be tested through the “standard methods”.
IMO, the scientific method is very useful and has led to many advances that have made our lives more pleasant — that is its main purpose.
However, to teach kids about fundamental issues (origins of the universe, eternity, life, etc.) through the scientific method exclusively fundamentally distorts reality.