Consequences of inbreeding doesn't probably exist in their clan. Maybe some gene prevents these genetic defects or at the very least minimizes it (This is present in some real world animals btw). Its theoretically impossible for a small population who are very closely related to persevere for long in the first place.
Its perfectly reasonable for the MC to run away since he genuinely does not like his sister in a romantic way, and the father was impossible to reason with.