So OK, they are biologically slightly less evolved than the Valakians and due to their model of coexistence the Menk do not need to be particularly intelligent. Without the Valakians around they have to solve more problems and due to natural selection their brains should grow.
But there's every chance that the Menk growth could be stunted if the Valakians die off. It's possible that the presence of the Valakians was what pushed the Menk to grow in the first place.
A younger sibling trying to keep up with the older one.
Social structures are fleeting. Once the Menk reach that point of being on equal footing, the society they live in will have to recognize that and adjust.
Starfleet is duty bound to attempt to assist those that ask for it. They are not permitted to mess in the social structure of a given world because its values do not match up with Starfleet's. Nor is it Starfleet's right to attach societal changes as a condition of help.