It would be wise of them not to go against those that know how to build alternatives. Never under estimate the stubbornness of a programmer wronged.
Look at Richard Stallman, disliked proprietary software so much he spent his life fighting it even building large parts of an OS! Messing with Github would be like creating 100,000 Stallmans - and I don't think anyone wants that. ;)
GitHub as a tool is easily replaceable. GitHub as a platform where you can easily interact with countless projects is not. MS would have to really fuck up to negate the network effects.
If MS did something super sketchy with Github, I suspect there would be an almost cambrian explosion of new tools to do with Github does.