It harms the opportunity cost of the projects that reside within it. That's a real harm.
And I think the point is that while GitHub is there, use it. If it closes off, or goes bust, migrate. You can extract all your data - keep a backup elsewhere. At worst, you can move to Gitorious. I mean, currently they use JIRA for bug tracking - that's not an open project either, that's run by Atlassian.