It has always been my opinion that the PD was part of the anti-Viet Nam war theme of the original series. (STTOS)
There were several episodes that realy played out this theme like A Private Little War. I have always thought it strange that the PD is diametricly opposed to the opening monologue ‘to seek out new life’. What the heck are they supposed to do seek out new life and watch it from afar? (like in Insurrection?) Also another thing to keep in mind is that all Star Trek series have multiple writers and they actually accept script submissions from anyone. The Trouble with Tribbles was written by a college student and he introduced money (they had to buy the tribbles) even though people in the Federation aren’t supposed to have money. Having all these different writers working on their own stories you are bound to have some inconsistent themes or ideas. But then again you can get some great stories if they aren’t written by committee.
If you only watch The Original Series, then, in that series, the Prime Directive was very poorly and patchily applied.
In The Next Generation (the one with Picard), it was used much more sensibly, and discussed in a more candid way (within the show of course)