Asking because I’m genuinely interested in a solution: Is there a way to design a HR department against this?

For your own company, how would you set up a HR function that does not have this tendency?

You wouldn't have an HR department as they currently exist, imo. Too many companies lump too many roles into that space because they don't fit need buckets besides "people stuff." Like just split of disputes into a department like you would compliance or an outside auditor.

But honestly it's an organizational systems and behavioral science problem. Look at the trends of HR problems that cause risk to the business (either directly through settlement or brand harm, or indirectly by losing good talent, also personal risk like being able to sleep at night), then isolate the feedback loops that allow the discord to amplify and eliminate them. So go trawl some unis that have systems researchers and spend money on IO psychologists, also listen to them because they're better educated on the subject than most business folks.

It’s called a “union.”

I wish they taught this in college because if you have to learn it on your own, it's a painful lesson.

They clearly failed at that.

But I have to agree with the general theme of what you're saying--HR will always try to suppress the victim.