the mac will recreate them everytime, so i'm not sure that's going to save you much grief.
the only way to avoid it on a mac is to format HFS+, which would solve the problem from mac to mac...
but unfortunately then the mixer wouldn't be able to use the card, since it requires fat32.
you can of course plug the card into a windows machine and delete the files...
(the mac would rebuild them next time you use it on the mac)
the better suggestion would be to modify the m20d firmware (or at least the media player part) to ignore files that start with ._
but clearly that's out of our hands :)