Agreed this will impact some organizations in negative ways such as the non-for-profit orgs. To that Github offers support in this sense here: https://github.com/nonprofit

Like others, without specific data, I would assume this will impact the majority of users on Github for the better and that organizations with many contributors needing access to private repos are the minority. In any pricing structure change, there is always going to be a minority that is impacted negatively. I don't think Github would have made this decision without analytics to back it up.

Another fair point is I think this structure is more appealing to companies who prefer to look at cost-per-employee for something that is an everyday tool rather than cost-of-architecture.