GitHub is primarily a development tool, so it should be designed for developers. Hierarchies align very well with development tasks, so it's natural to use them for development tools. That other people don't grasp them is not relevant for GitHub.
Also, the three most common navigation tasks I do are "go to the code", "go to the issues" and "go to the pull requests." Those are also the first three tabs at the top of the hierarchy. I don't think that's an accident; I think the designers at GitHub designed the layout so that the most common tasks are on top and first. In other words, they designed GitHub like a tool, not a normal webpage.
With this redesign, I'm going to constantly have to find the "Issues" and "Pull Requests" tabs among a sea of others. That's not good usability.
I've thought that maybe the markdownified README should be flipped up on top, but even that I think is counter-productive. When I'm working with a GitHub project, I commonly want to load up the page and navigate to some files. If not, it's usually not much scrolling to get down to the README. But READMEs can be quite long (which is a good thing), and it would sometimes be a pain to always scroll past them to get to the files. The better solution for that is a good project page.