Because US government is against cryptocurrencies. As long as Microsoft doesn't want to have problems with officials they won't take any risks. Especially risks like that: Bitcoin as a payment method is only for geeks and it's not worth keeping it just to satisfy them.
The main reason for microsoft to remove bitcoin as a mode of payment is simply because of their high transaction charges and expect these sort of news from other companies too as people wont be using bitcoin as a mode of payment anymore until there is a permanent fix with the implementation of lightning network and after that these companies might rethink of accepting bitcoin again.