So while I agree that an open and distributed system that does what github is currently doing would be better, I don't think that github's popularity and eventual demise is as terrible as you claim.
Trying to figure out which of these scenarios (or a different one!) is going to happen sure looks like optimizing prematurely to me, in particular so long as there does exist some fashion of a backup repository.
Planning in the 20 or 50 years range is counter-productive.
Heck, whole countries might not exist by that time (the same way ex-USSR and Eastern European countries split into different ones).
Now you have me thinking about how to plan that long! You would need an architecture easy to port and good documentation...
Or become so important that old platforms are maintained for your sake!