The Prime Directive was intended as a principle of non-interference. When TNG came out we were coming out of the cold war and only two decades removed from Vietnam, it was meant as a principle not to force the Federation's ideals onto other cultures and cause another Vietnam.
In Pen Pals, I believe the writers misinterpreted it as a directive not to save entire civilizations from natural disasters based on the specious logic that one of them might become the next Hitler.
I don't think they misinterpreted it really. They just made it more restrictive to generate more drama on the show.