If they wanted to do an episode about the formation of the Prime Directive they should have done one where Archer intervenes on a planet because it seemed like a good idea at the time and a couple of episodes later the decision completely backfires with negative repercussions not only for the planet in question but for Earth as well.
If I was going to Modify "Dear Doctor" to fit this criteria. I'd have the planet in a strategically valuable for Earth, but Earth can't use it because it's occupied. Being nice guys Archer and Phlox give them the cure for the disease. However, they don't get it quite right so about a month later it turns out they have created a even more virulent plague that wipes out both species completely. The planet is now free for Earth to use as they see fit. All the other local powers think Earth committed genocide on purpose. That would cause the formation on a stringent Prime Directive very quickly.