I think it's fine for awards to help push movies with a message (or a message with a movie) because films are not made in a vacuum and will end up somehow say something about the times more often than not. I mean Moonlight is apparently a fine film on its own, and it's no less or no more out of place in the arbitrary selection of the "best films of year X," than any of its peers. If voters wanted to honor a good film and also take a stand on whatever issue it depitcs, well good for them.
Most of the time, I feel any debate on the matter comes from a sense of overestimating the meaning or importance of those awards.