"tie you up" might have been better written as "lock you in". Those tools can certainly be made available through other means via free (as in freedom) software. It takes work in doing so and that's what Github is selling - ease and convenience.

Github has obviously done a great job of making these tools useful and approachable. The point about having ultimate control over that data though is valid. Github might be able to mitigate some of these concerns with something like Google's "Data Liberation Front", providing a contractual agreement with users to make their data easily exportable if they choose to do so. Of course, even that may not be enough for some projects and for them it's a totally valid option to avoid github (and similar closed SaaS options).