To be honest, I don't think GitHub is to be blamed for how scientists use it. AFAIK there are data repositories more suitable for the purpose of sharing data sets and metadata, and out of the hands of big corporations (but may subject to big governments), e.g., Zenodo (funded by CERN) and DataONE (funded by NSF). Zenodo can even generate a DOI for your data set, which GitHub does not do.
That being said, I think this Nature report adds nothing new to the narrative. Sure, open science is great, but who's gonna pay for it? Neither GitHub nor Microsoft is a charity. Since most of the research mentioned in this article are funded by government, they should go to the data repositories that are designed to store data derived from publicly funded research. GitHub just wasn't designed for that purpose.
That being said, I think this Nature report adds nothing new to the narrative. Sure, open science is great, but who's gonna pay for it? Neither GitHub nor Microsoft is a charity. Since most of the research mentioned in this article are funded by government, they should go to the data repositories that are designed to store data derived from publicly funded research. GitHub just wasn't designed for that purpose.