I mean.. Ideally you wouldn't need to store any user keys and just have users sign functions requiring authentication. This business idea makes more sense if it's a sort of HIVE tipping on Github rather than what the naming implies.

There was a project / site called utopian.io that did some github related stuff with code and whatnot. You might dig through the rubble of that one to see if any useful parts or ideas for yours will work.