While non-interference is the Prime Directive, active interference would seem to be TOS Starfleet's actual general policy. The Starfleet Admiralty, and the Federation council might not alway see eye to eye, on every matter.
Discussions between the Enterprise D's officers during the episodes Symbiosis and Pen Pals shows that exactly what the Prime Directive means isn't completely clear even among senior Starfleet officers in the 24th century.
The prime directive would seem to be more of a political directive than a carved in stone constitutional thing, it is shown to change over the course of the multiple series, sometimes obviously between adjacent episodes.
Possibly the prime directive is considered part of the Federation membership's collective foreign policy, as various council Presidents and foreign secretaries come and go the Prime Directive get reinterpreted, rewritten and it various sections assigned new and different levels of priorities. When necessary Starfleet Captains receive the latest updates and revisions.
In Bread And Circuses, Spock asked Kirk "Then the Prime Directive is in full force, Captain?" Which suggest that it just might not be "in full force." And determining authority would be Captain Kirk himself. Or maybe Kirk would be the one to have been advised of the most resent update in the never ending revisions to the PD.