I actually sent them a support ticket about this, and this was their reply:
"I understand how the previous workflow would be useful, and we apologize for the inconvenience it has caused.
However, the good news is that the mobile team is working on releasing iOS and Android GitHub mobile applications early next year, which should resolve some of the limitations of the current mobile site."
Like really, just give me the desktop view back ffs.
(This is with YouTube set to request desktop site always in settings).
Totally agree with you here. Lots of other sites link to GitHub and being pulled out of the browser and into a native app is just not a good user experience. I've uninstalled Facebook and Twitter the same reason, and I enjoy using the social sites a lot more now.