Alright, I posted an update.
I had a bug, where if you tried to delete a harmony button, which can't be done, it would actually corrupt your configuration. If you have ever done this, you should do a clear configuration and start over again. I'm really sorry about that. When I started digging into the code, I noticed that issue.
Here is how it works, and it's a bit half baked, not completely what I want.
I want to catch the use case for when a user gets a harmony remote, they load the flirc proflie on their harmony, and everything works out of the box with flirc and no additional software is required. In other words, the harmony-xbmc profile is and will be enabled by default.
If you want to re-purpose one of the flirc harmony-xbmc keys, you can. That key will take precedence over what's currently in read only memory. You can delete the newly mapped key, and functionality will restore to the default key. If you try to delete the default, the gui will report that the key must have already been deleted, it's not found. (this is not ideal, I need a proper error code but didn't have time, I needed to get this release out because of the bug).
You can disable the harmony profile entirely in the advanced menu. I've created an option for that as well as added an appropriate commandline setting.
The flirc_util in the mac GUI is now statically built, so you wont get a missing libusb-1.0 library anymore.
I really think you did a good job explaining this. I will try to polish the next release so that 1-4 are implemented to your description.
As far as your desire for another profile. Yes, I promise that I will try and get a plex, wmc, and eyetv profile for the harmony in as soon as I can.