obviously there are alternatives to github. gitosis for one, sourceforge is still there, repo.or.cz is nice and old school as well, and atlassian has bitbucket i think (though ive not used it)
perhaps there is an opportunity there to team up with a less known code hosting provider, or start one (perhaps using gitolite or other open source code) and bring the duckduckgo magic to code hosting.
And even if those problems actually where common, they alone can't be used as an argument to migrate to an alternative. It is simply not relevant which problems other projects runs into when using GitHub, the only thing that is relevant is what problems DDG run into. If DDG have the problems stated above, then it's relevant, not else.
actually, git makes it incredibly simple to jump from hosting platform to hosting platform. and with your web content on a branch its even easier.
its very common to see projects using both github and sourceforge, and also common to see them having a backup on repo.or.cz
anyway, its an idea and i understand that its quite far way from the core searching function of duck duck go. but i think that the problem i have highlighted is a real one and one that can be exploited to provide a differentiated product