The way I see it is, Archer and crew were morally and ethically bound to help the Valakians. To willingly withhold a cure for a disease that you know is killing people is to become responsible for everyone who dies from that disease.
And in the end, the Valakians ASKED for help. So even if there had been a Prime Directive, that alone would have rendered it irrelevant. The PD allows one to render aid to anyone who asks for it. The Valakians may not have had warp capability, but they were already aware of Earth, and thus the PD goes out the window.
To withhold aid because the Valakians MIGHT one day become some kind of evil empire is just casting at straws. No one has any idea what that species will evolve into. The future is irrelevant; all that matters is the present.
This is also why I really couldn't give two shits what happens to the Menk. The Menk are not dying; they are not being struck by a deadly plague. They don't need help. The Valakians do. To deliberately allow - even encourage - the Valakians to die because the Menk supposedly deserve to live more than they do, is IN ITSELF interference. It's choosing one species over another. Archer is already intefering even if he does nothing!