Github wants to price discriminate between serious users who can afford to pay more, and casual users. Projects with a high development budget (e.g. complex software projects) don't necessarily use more disk space than someone's personal website, so disk space isn't a good way of price discriminating.

On the other hand, organizations with a high dev tool budget are probably more likely, on average, to have more private repos. So it's in Github's best interest to charge by repo count, until they figure out a better way of discriminating between customers.