Honestly, to me, these signify more of a problem with either a) legal interpretation of these licenses or b) the licenses themselves. The things that Github wants to do with your code are perfectly reasonable, and I don't think would be interpreted as "breaking the license". All code is attributed to you when displayed to other users and isn't being broken up in its distribution (unless you believe that only viewing a single file is breaking up the source code... which is just silly) in practice.
I really don't view this as a problem. I think fighting any of these issues against Github (without this ToS) in court would likely be very difficult and unfruitful... but the risk makes it necessary for Github to protect themselves anyways.