He wasn't definitively saying he favored the Menk. He was saying that there were factors worth considering on both sides of the argument and he wasn't prepared to favor the Valakians at the risk of condemning the Menk. His decision was not to act in favor of either side, but to let natural evolution take its course.
Condemning the Menk to what exactly? That's the second time you've asserted that the Menk are in some kind of trouble, yet that isn't in the episode at all.
As far as 'natural evolution', the Valakians evolved to a state where they had the ability to ask for help.