So... you're saying that the good guys should be complicit in genocide of sapient species that haven't reached a certain level of technology for no reason? Especially when, in this case, noninterference would likely result in the end of coexistence between two species and the genocide of one by the more advanced species that just got told "we think the other guys are going to advance once you're all dead and gone, so we're not going to help you"?
Also, the lesson I got from the beginning of into Darkness is that the Prime Directive is a morally reprehensible regulation that compels captains to let species die from easily solvable natural disasters. It honestly made me wonder why they kept going on about the Admiral being evil for militarizing the fleet when Starfleet was letting people die horrible deaths for no reason.
The Federation doesn't have the resources to save every single non-warp-capable species out there from every disaster they can and will face, and even if they could, they would then be indirectly responsible for the consequences of their interference. If you do "the right thing" and save a planet of people who then become bent on conquering the galaxy, are you willing to take responsibility for cleaning up the mess you created?
The Prime Directive isn't about morality, and if it is, it's certainly not about -human- morality, nor should it be, because if there is a universal morality it most certainly isn't defined exclusively by humanity. It's about Starfleet trying to do what it thinks is for the best with regards to advancing civilizations on a galactic scale, and creating a policy that frees its captains from needing to make decisions that can't possibly take all of the variables into account. What's the longest we ever saw Our Heroes studying a pre-warp civilization? Do you really think that's enough time to understand all of the dynamics in play on an entire planet??
Given that we clearly see that Kirk's interference in ID -has- altered the evolution of that civilization, I think an argument could be made that in a sense they -have- died. Whatever they might have been is no longer what they will be. Is that better than being dead? Well, maybe, but it's clearly not as optimal a solution as them being saved without becoming aware of extraterrestrials.
Hell, how would we feel if aliens showed up on Earth one day and decided that dolphins were meant to be the dominant species...so they were going to actively give the dolphins a hand by wiping out humanity? Probably not so hot.
It's all well and good to say Our Heroes should interfere until you consider how the species that (inadvertently or otherwise) suffer from that interference might feel about it.