The link on GitHub to the real site is marked with rel="nofollow". I wonder if it would make sense for GitHub to remove nofollow in some circumstances. Perhaps based on some sort of reputation system or if the site links back to the repo with a <link rel="self" href="..." /> in the header? Presumably that would help the real site rank higher when the repo ranks highly.
I don't see any reason that GitHub should use rel="nofollow"
Github only has authority because people put their shit there; if people want to point that back at the "right" website, Github should be helping facilitate that, instead of trying to help Google make their dogshit search index any better.
I mean, seriously, doesn't Bing own Github anyway?