Crimea was unilaterally annexed after a military invasion; the sanctions are intended to maintain the idea that it belongs to Ukraine, not Russia.
I actually don't object to sanctioning the area - it is less aggressive than sanctioning all of Russia, and Russians entering Crimea against the wishes of the Ukrainian government could be seen as invaders. After all, the original invasion was done under the cover of "mercenary separatists" who did not identify themselves as the soldiers that they were. And let's not forget, those "separatists" did also shoot down a civilian airliner with a Russian anti-air missile, killing hundreds.
Personally, I would prefer that organizations like Github remain impartial to this sort of thing, but they aren't discriminating against Crimea in particular; they're applying the same "it's out of our hands" attitude as they do for developers from areas with similar sanctions, such as Iran.
