I personally consider the Prime Directive fairly clear (more a response to the thread as a whole than to you in particular on this point). Data violated the Prime Directive when he rescued that kid in Pen Pals and the Enterprise as a whole prooobably bent it pretty hard saving their planet since the dominant form of life was apparently doomed to extinction.
Someone else broke the Prime Directive in Who Watches The Watchers and Picard was left with two crappy choices ... a) let the violation set their society back or b) correct the setback by violating a bit more. Even when I was a Christian, I felt Picard made the right choice. Whether a review board would agree, I can only guess.
I feel like the writers sacrificed characterization for plot expediency with regards to Into Darkness.
Jim Kirk is many things. Largely a terrible person? Yeah. Willing to break the prime directive for a friend or for someone he's got the hots for? Hell yes. Willing to break the prime directive for a species the universe has arbitrarily decided should probably die for arbitrary reasons when he doesn't know anyone on the planet and ultimately considers them inferior? No fucking way.
They needed Jim in hot water to give a reason for him to deal with some other shit so they completely fucked over his characterization. I didn't even get past the first scene before being pissed off.
I can deal with changing canon. I can even deal with changing characterization if the new characterization is interesting. This wasn't a change. It was just horse hockey.
Bringing things back into the realm of theory and speculation, one wonders if they have an exception to the Prime Directive which allows them to interfere with formerly advanced cultures who have been artificially thrown into a less advanced state by another more advanced state. It would allow for a lot of TOS Kirk stuff to be ok (if it was ok) and explain why messing with Kess's people was ok.
In other news, these spoiler tags are pretty awesome.