Unlike in cities where the decisions regarding marriage etc. are taken by the person involved or the immediate families, in villages it is the society which dictates.
So far from Mukhi's and Aru's character it is revealed that Mukhi is not the kind who will hold personal grudge against Aru if her sister runs away. Even Aru is not a martyr by nature. But the rules of how society functions are different in villages and Mukhi cannot take a decision which is not consistent with village Panchayat. He cannot let his personal opinion rule his decisions.
So even if he personally did sympathise with Aru and family, he may have to take a decisions for marriage as per panchayat laws.