Well revealing "The Secret" itself carries with it the implied threat of being burned as a witch, or at the very least taken away, and being poked, prodded and experimented on which isn't exactly physically safe...
As for "reading thing into it," I honestly think people aren't reading nearly enough. Being too focused on the Superman mythos and what his powers are and all you're ignoring the subtext of the movie, because Clark in MoS is a metaphor for "the other" in our society, people who are different and marginalized for their difference, be it gender, sexuality, color of their skin, religion, nationality... people who don't fit in what society deems "normal." The Kents are blessed with a child who they see is beautiful and special and unique, but at the same time are aware that society shuns and fears difference, which is sadly an increasingly relevant angle to this take on Superman, and they're trying to navigate that reality as best they can and make sure their child has a semblance of a normal childhood.