I've always been broadly under the impression that the HR department was a waste of air, but I suppose conflict resolution is perhaps something they'd be useful for.
HR, legal, finance and IT are all unpopular for the same reason: it's part of their job to stop you doing things that may get the company in trouble later.
Of course, this means they may be at times too conservative in the interests of having an easy life. Doesn't mean they're not useful at all.
I find myself almost perpetually annoyed by the bureaucratic arms of big organisations, HR and IT in particular, but what you've written is, in my view, a (terrible ;-)) truth.
I think a balance of conservative and progressive opinion is required for almost any organisation to operate effectively: (genunie) progressives drive us forward, and (genuine) conservatives stop us going over the cliff - it is pretty much as simple as that. Unfortunately, finding the appropriate balance for any particular situation can be extremely tricky, so largely we get it wrong, and just stumble along, grumbling to ourselves about how stupid and ineffective everything is.
On the assumption that there are genuine problems within Github, hopefully this situation will at least give them a chance to engage in a bit of rebalancing, and find a more sustainable path for their future. This is, of course, the problem of solving problems by trial and error - you have to deal with the errors, and in cases like this the errors can be quite painful for the people involved.
My takeaway is that the most important aspect is process. Conservative or progressive may be less important (although it is probably easier to come up with a conservative process that is workable, simply because that's where the hive-mind will be). But if you don't even have documented process, you won't even be able to know where the problems really are when they arise.
IT isn't unpopular when done right. IT exists to help people get shit done, and they need to explain clearly when they can't why they can't. And can't better have a business reason (higher priorities, funding channeled elsewhere, etc.).
The problem with legal is that the safe position is always "no". So, finding legal who understands that businesses sometimes have to take a risk, and we need to know if this is "illegal" as opposed to "inadvisable, because it's going to cost money" as opposed to "inadvisable, because it might cost money but might be worth the payoff" is not easy.
HR is simply useless. It's only useful tasks are all effectively part of "legal". It can't make useful decisions on hiring and actually gets in the way. Any employee with a genuine grievance knows that HR is the companies rep, not yours. Oh, and they generally have access to a whole bunch of things that stir up hideous amounts of politics (salaries, reviews, promotions, etc.) So, what's left that's useful? Nothing.
At my previous job I thought the same thing. They didn't stop people being bullied by superiors and basically did nothing but exit interviews and layoffs. The entire company was really dysfunctional.
At my current job HR is _supremely_ competent. The entire organization is more functional and a joy to work for. I think there are subtle but significant effects when people know that it is not okay to behave in a bullying or discriminatory manner because HR takes those things seriously.
The main job of HR is prevent the company from entering lawsuits with (former) employees. Anything else is just window dressing. Most HR organizations like to act like they are an impartial judge in conflict situations, but they're on the company payroll after all.
So while for a single employee HR might seem like a waste of air, it's elementary for any business with a reasonable number of employees.
While you are right to note that the person signing your checks holds many of the strings, it is also true that each employee is an autonomous unit with values that they live by and advocate for, resources that they control and steward, and a contract for value exchanged.
An HR department absolutely works to protect the company, but a good HR department will also work to protect the employees, because in the long view that is also beneficial to the company. And many HR people who I've talked to specifically enjoy their jobs because they like working to make employees lives better. Where their directives conflict with that they will try to fight the directives.
Certainly in some cases where there is a unresolvable conflict between employee and employer, HR will work against the employee. But for a good HR department those situations should be very few. A good HR department will be able to project forward into a long enough view that they can find ways to move forward amicably that protect both the employee and the employer, to everyone's benefit.
Well there is also a whole bunch of really boring mundane tasks that take a lot of time, such as setting up and supporting health insurance plans, getting people into various directories, organizing the interviews, etc etc. I may look down on HR at times but boy am I glad we have them to do these things.
Past a certain size, it's nice to have an HR professional managing the company's treatment of its employees. It's also nice to have a third party/person available for conflict management.
...maybe.