No, in TOS it applied ONLY to pre-warp civilizations - as in, it exists to ensure their natural development. It's TNG and beyond that suddenly says; hey, you know what, it applies to everyone! Yay!
Just because someone, Starfleet Command or the Federation Council decided that the benefits for breaking the Prime Directive outweigh the drawbacks, does not mean that the Prime Directive does not exist.
It's during TNG times and beyond that they elevated the PD to an unbreakable religious law to be broken at the peril of burning in hell. During TOS, they treated it, rightly, as guideline that could, and should be broken if it was required, but only with the utmost caution.