It was mentioned up-thread somewhere that each time the Elements of Harmony are activated it weakens Calice's hold. Is there a way for this knowledge to become known in-game, or something similar along those lines without breaking anything?

I think this is a great suggestion for helping the tone. If it comes to light that activating the Elements helps, it will in turn motivate characters to make a goal of learning more about the Elements. (Not too unlike Twilight's discoveries on friendship when you think about it.) In turn plots revolving around strengthening the Elements of Friendship will naturally be lighter-hearted and closer to MLP canon.