FASA had an instance of the first Starfleet captain being held accountable under the PD. He came across a primitive world whose two major powers were about to destroy themselves through war, and he used his starship's weapons to destroy theirs so that they wouldn't annihilate each other. Starfleet ultimately found him guilty of violating the directive and took his command, even though they acknowledged his sentiments were good.
I tend to agree with you, though. While there are certainly circumstances where it would be be best to avoid direct contact or interference with a more "primitive" culture, it wouldn't be entirely avoidable or undesirable. The Capellans from "Friday's Child" would certainly fit into such a category, and yet they were valuable trading partners to both the Feds and the Klingons because of their minerals.