I am not too worried for one reason only. Whether you like Microsoft or not, they didn't get where they are by being stupid. I don't think they would change the things that make MC so successful like modding. They allow plenty of modding to games they already own or even created in house. I mostly expect them to clean up the code and make it more efficient as well as more public marketing to expand the user base. Why would they change something that is so profitable when any changes would drive away users.
My only real concern is their greedy ways. When I bought MC, Mojang made it my understanding that it was forever. I hope they don't decide to start charging for updates or DLC's.