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This could lead to all sorts of conflicts. Imagine the Doctor using his TARDIS to save a primitive society from a nuclear blast. Now imagine there’s a Starfleet starship secretly watching in orbit!
I don't see any conflict there. Starfleet: "Phew. I was worried I might have to either break the rules or watch a civilization destroy itself. I'm sure glad things worked themselves out." Even the most legalistic nit-picker would take action. That time lord is not a federation citizen. Now, if the time lord was doing BAD things, they might work themselves up to "protect the vulnerable civilization from outside influence." Or they might not... it depends whose writing this episode. (note: the version of the Prime Directive in the Player's Handbook [thanks Don] is still true to the Star Trek ethos, but it doesn't go so insanely far as certain interpretations go. More importantly, it fits what we see in the episodes.)