This seems to me to be the major takeaway for organisations outside github from this sorry affair. I'm sort of surprised you are the only person to raise this so far.
In the UK, the employee who resigned could have a successful day in an employment tribunal. And one aspect of the hearing would be privacy and the Regulation of Investigatory Powers Act provisions.
The right to be sued for libel whenever they write something that someone else doesn't like?
Employment rights however are slightly better. The employee interviewed in the OA would have recourse to an employment tribunal for what used to be called 'constructive dismissal' - the terminology may have changed recently. The monetary compensation would be quite basic by Valley standards, but the public exposure of the employers, subject to cross-examination, would be most satisfying I imagine.
Get all their details, and complain if you think you were treated unfairly.
Unfortunately, this doesn't invalidate the fact that you're correct in a way. If Simon Singh hadn't been able to afford the time and money to defend this case, the libel suit would probably have stood.
Still, it's a step in the right direction, and an important legal precedent.
If this happened in my company, lawyers would be crafting a settlement right now.