I imagine this isn't going to be a very popular opinion, but...
I almost think people get too hung up on the use of the word "evolution" and essentially end up overlooking the forest for the trees.
My understanding of the Prime Directive...which granted doesn't exist here...is that the Federation shouldn't be interfering in the development of civilizations.
By that standard then, all that really matters is that the Valakians are confronted with a disease they're unable to cure, and that if Our Heroes were to cure them it would (possibly) alter the development of the civilizations on the planet. It's obviously hard to say for sure...for all we know the Valakians could develop a cure the day after Our Heroes leave.
If the Federation really believes in a policy of non-interference, then it doesn't ultimately matter whether the Menk are there or not. Non-interfering in this case means not allowing the Valakians to persevere through means that they couldn't develop without Our Heroes' assistance.
Hell, it could just as easily be argued that the virus has a right to exist and would ultimately "evolve" to be the dominant life form on the planet...curing the Valakians means committing genocide at that point, if you really want to look at it that way.
In any case, it's a mistake to approach the Prime Directive as a moral issue, because adhering to the PD ultimately means you have to leave your morality at the door. Heck, the beginning of Into Darkness makes this abundantly clear.