I don't have any numbers on how people structure their accounts on Github, but my feeling is that this is a positive change for the majority of Github users.
Git encourages having many smaller repos for modules over massive single repos. $1/repo/month is fine for active projects, but gets expensive really fast if you want to keep archives of small private experiments around. Because of the per-repo pricing on Github, I've seen many friends and startups I've worked with keeping their open-source public repos on Github (for free), while moving private repos to Bitbucket.
I would not be surprised if this pricing change would be a net revenue loss for Github, but still implemented to avoid losing market share to Bitbucket.