This is the one episode in which the message and the premise really does not make sense with the series' own universe, which was Twilight's skepticism of the supernatural. MLP:FiM is an universe in which was well established that the supernatural is real, plus Twilight herself spellcasting talking unicorn nonetheless. The premise would work better in a sci-fi universe, like Star Trek, but it really looks forced in a magical universe.
At least the writer was more or less aware of that paradox with Twilight, and hand waved it by having Twilight to say something in the lines that true magic comes from the heart and yadda yadda. This still is vague and not enough to justify, did Twilight mean that she is skeptical of non-unicorn ponies using magic? Or of magic coming also from potions? Nothing of this was stated, this is just headcanon, in other words, the viewer making the writer's job. Plus Twilight specifically shows disbelief of the supernatural while she has supernatural powers herself. Magic in MLP was never established as "sufficiently advanced science", it was always just regular magic.
But let's for a second ignore that the moral of the story contradicts the very own story. This still shows a double standard when it comes to TV and entertainment in general: morals that go against a spiritual worldview are acceptable, while morals that are favorable to it are deemed "offensive". A future episode, Feeling Pinkie Keen, regardless of what Lauren Faust said afterwards, had a clear moral favorable to faith. And then the Internet Thought Police™ lashed out on that episode exactly because of it having a spiritual message. On the other hand, Bridle Gossip having a materialistic message is acceptable to them...
I am a religious person myself, but I can accept a nonreligious message in a story for the sake of the Freedom of Speech. What I do not like is when a story have to contradict itself in order to force a specific message, this sacrifices part of the entertainment value of the story. The story itself is more important than the message it is trying to convey, and the story itself does not even need a message, it only needs to be entertaining.
Having Twilight from MLP to be skeptical of the supernatural makes as much sense as having Dr. Spock from Star Trek saying "a wizard did it".