Monkey's Audio is not supported and will not be supported as long as there is not a decent license attached to the source code. Besides that, the fact that FLAC is a better general answer (works much better on embedded devices) means FLAC is better. It is a possibility that one day dynamic audio input plugins will be added to MPD but even then according to the Monkey's Audio license, which is unclear at best, it will probably still be illegal to distribute such a binary.
There are moves by the gstreamer team to get Monkey's Audio LGPL'd, but there has been no answer from Monkey's Audios' author.
Also, even if it _were_ allowd, it probably wouldn't happen unless there were developer interest due to it being inferior to flac.