It seems perfectly plausible that debian packages are mostly GPL while github is mostly MIT. (Eg Github first became popular in the ruby/rails community which tends to skew more MIT and corporate-friendly). I don't at all see the implication that the difference means someone's trying to lie with statistics.
The lies comes from people who uses the statistic to prove a change in society. The statistics is, as always, just data that is relevant in a specific context.
As to why github is mostly MIT, a reason I read is that github replaced private cvs, ftp and folders on ones laptop with a web service that has the dual functionality of work platform and collaboration platform. It follow the same path when people moved away from using office programs and started to use google docs.
