Questioning authority doesn't make you rational, it just makes you the kind of person that questions authority. I think there has undoubtedly been selective pressures created by society that have increased the tendency to conform (capital punishment is basically a multi-century long accidental project in eugenics).
We have to decide what we mean by rationality. Choosing to conform, or at least be careful about how you rock the boat, seems like a rational course of action. Loudly telling everyone you know that the king is an idiot doesn't seem too rational to me, even if the king is an idiot. Remember, Galileo didn't get locked up for saying the Earth revolved around the sun - he was locked up for publicly insulting and humiliating the Pope.
Selective pressures have likely worked (IMO) to make us more mindful of the status quo, and hesitant to upset it, regardless of rationality. This means that if you have a rational reason to oppose the status quo you are less likely to act on it; it also means that if you have a completely irrational reason to oppose the status quo you are less likely to act on it. Over all this is a socially stabilizing effect.
I suppose if there are gene variants associated with higher levels of conformity and we can show that they have been increasing in the population over time that would provide some evidence. The closest thing to that I can think of is the evidence that dogmatism is a heritable trait. Is there evidence that dogmatism is increasing over time?