@1Referee. I reckon it would be smarter for the Github founders to only accept a deal if the payment was in bitcoins. They might receive billions lower but they will make billions more by holding bitcoin than holding Microsoft stock hehehe.
GitHub itself and the shareholders don't have much to do with Bitcoin, so it wouldn't work. Accepting Bitcoin would mean they expose themselves to the risk of devaluation of their Bitcoins, and that risk isn't something you want to be taking with a multi billion dollar company. There is simply too much at stake.
Another factor why such a deal doesn't work on this level is that Microsoft would have to obtain billions worth of Bitcoin one way or another, which is a rather difficult task. Assuming the cash settled value would be close to $5 billion, it would require Microsoft to buy like ~660,000BTC. You can't even buy 100,000BTC through exchanges due to how thin the market is. It would require high level OTC connections, and then it's still incredibly difficult to come close to that number of coins.