I just love the deliciously polarized rhetoric in this thread. Folks are taking all sorts or pot-shots at TOS and at each other. All the merry while, there are a couple of things conspicuously absent:
Consider the TNG ep "The Drumhead"...
During the inquisition of Captain Picard, retired admiral Norah Satie poses a question, really a polemic, to the captain; accusing Picard of violating the Prime Directive nine times. Picard defends himself, insisting that in each instance his command decisions were justified.
This, coupled with Picard's statement at the end of "Justice", the "no laws are absolute... even life itself is an exercise in exceptions" should indicate that there are indeed loopholes or allowances built-into Federation law and Prime Directive that make overriding such regulations possible.
And in "Angel One", there is the suggestion that the survivors of the ill-fated civilian vessel Odin are not bound by Starfleet regulations, and thus Ramsey and others openly lived among the natives for some time.
Of course, one need not look to TNG to find these instances. Consider "A Taste of Armageddon" and "Friday's Child":
In "Taste", Ambassador Fox orders Kirk to pilot the Starship Enterprise to Eminiar VII, saying "thousands of lives have been lost", and Fox intends to intervene to stop this ongoing problem. Also: Spock suggests the possibility of the U.S.S. Valiant falling victim to the Eminian war.
In "Friday's", Kirk obviously has orders to secure a mining treaty with the inhabitants of Capella IV in order to acquire the valuable mineral Topaline. Again, Kirk is obviously under orders to establish a Federation presence on Capella IV, and in direct competition with the Klingons, no less. There is no discussion of non-interference regulations applying to Capella IV, as if the Prime Directive has been rendered moot.
These instances make it clear that there are exceptions to a strict adherence either written into the Prime Directive, or somehow allowances are made by Starfleet Command that relieve starship personnel of this regulatory responsibility.
Keep in mind that in "Bread and Circuses" we hear Kirk and McCoy quoting what is obviously a passage from Starfleet General Order One, but we by no means have the entire text of that regulation.