How would you handle this case if the work you're doing that's being stored on private GitHub repositories wasn't on GitHub at all (like the majority of tech work that employees do for their employer)?
The point is that it's not entirely useful for employers, which seems to be what you're concerned about. If 80% of people are committing to private corporate source control, and 20% are committing to private github accounts, it's not readily apparent why you would care to see some vague statistics about commit frequency for 20% of your candidates.