There's two steps to answering this question:
- Is there actually a credible legal issue here?
- Is that legal issue going to be a practical impediment to open source code on Github?
Is there really a legal issue here? What is it?
The issue described here is that if Bob posts Alice's open source code to Github, Github requires specific rights to the code that Alice may not have granted in her open source license. For example, Alice might license her code under the GPL and then say, "You granted rights to Github that I never gave you the right to grant (like to reproduce my code without attribution or reproduce it without necessary downstream GPL requirements); I'm suing you or issuing a DMCA takedown."
In short, Github now requires a license grant that is outside of the scope of what is required by the open source definition (or free software definition), so many open source licenses do not offer sufficient permission to allow someone other than the copyright holder to ensure that these rights can be offered to Github. Possibly these rights could fall under fair use or de minimis or some other justification, but they are certainly outside the explicit grant of many open source licenses, so this sounds like a legitimate legal concern.
The preconditions of legal trouble speculated in the article are
- Alice, the original author of a project, grants some rights to her project to Bob under an open source license
- Bob uploads that project to Github (as-is, or modified, or included inside another porject)
- Github requires rights outside the scope of the license that Alice granted to Bob; Bob wrongly affirms his ability to grant those rights by accepting the terms of service
- Alice decides to take legal action against Bob
If such legal action did take place, I cannot begin to speculate how a court would rule on it, but it's a credible concern.
This is not an issue for an original author like Alice, assuming she holds copyright on all of her code. Also, it's plausible (though I cannot say for sure) that if Alice has her code on Github already, then Bob can offer the rights Github requires (or perhaps does not need to offer them) since Github has them already via Alice. However, I cannot say for sure, and you certainly shouldn't rely on this barely-armchair analysis as legal advice if you're planning to put someone else's work on Github.
The FSF has a statement about the new Github terms saying that at worst they may be read in a way that is incompatible with the GPL, but hopefully not:
But licenses like the GNU GPL already give the necessary permissions to make, use, and modify local copies of a work. Are the new GitHub ToS asking for more than that? It's not fully clear. While the grant language could fit within the scope of the GPL, other words used in the section like "share" or "distribute" could be understood to mean something that wouldn't line up with the GPL's terms.
[...]
Because it's highly unlikely that GitHub intended to destroy their business model and user base, we don't read the ambiguity in the terms as granting or requiring overly broad permissions outside those already granted by the GPL. It would be inconsistent with changes they made last year on choosealicense.com to treat copyleft better. The relevant sections of the ToS seem to be just restatements of typical free license terms.
Is this legal issue a serious threat to the reuse of open source code on Github?
This is now pure crystal-ball speculation, but probably not. Looking at the legal analysis above, you'll see that Alice the author has to actually want the code to be gone from Github. In general people release code under an open source license because they want to share it. That's exactly what a downstream reuser like Bob is doing, so I'd expect that in the overwhelming majority of cases, there's no issue: Alice wanted her code to be shared and reused, and Github's terms of service don't materially interfere with that goal in any way.
The concessions that Github asks for -- to reproduce snippets of the code in a search feature, or reproduce the entire repository as part of the fork feature -- are so trivial that it's hard to image why Alice would go to the trouble of even doing so much as a DMCA takedown (never mind a full blown lawsuit). The most likely cases I would expect are that Alice has a vendetta against Bob or Github for some reason, or she doesn't like having code under the GPLv3 anymore (but it's explicitly irrevocable) and is trying to remove Bob's code in a fit of licencor's remorse. These don't seem like common cases; overall, open source development on Github will continue as usual.
Again, this is speculation, not legal advice, so don't come crying to me when you get sued (but do let me know -- I'd be interested in updating this answer). :)