apeman: I clearly can't speak to what GoG will do, but you should be able to get it working yourself since the Windows version uses DOSBox.
http://www.dosbox.com/
I tend to do this anyway even on Windows since I like to customize the DOSBox settings a bit beyond what GoG provides. This way I just do it once and then have a bunch of games installed in a directory that I mount as the virtual drive within DOSBox. However, if you just want to get things working as they do on Windows, I think the only thing you might need to adjust would be the [autoexec] section to point to the directory with the Master of Magic files, the syntax may be slightly different on OSX. It looks like they have used two separate .conf files for Master of Magic. dosboxMOM_single.conf is the one with the mount command and path. Then you'll just need to create a shortcut or shell script to invoke DOSBox, probably something like this:
DOSBox -conf mom/dosboxMOM.conf -conf mom/dosboxMOM_single.conf -noconsole -c exit
Again, the syntax for this may be somewhat different, this is untested!
Thanks for the tip! I´m currently playing MOO2, love that game, but when I feel like playing something else, and if GOG has not yet made it compatible, I will try this to make it work.