To be clear...MiniLyrics registering itself as a plugin doesn't give MC any control over it. It's not well integrated with MC—it opens and closes with MC, does it's thing, and provides its own global hotkey configuration.
I don't care about it running in the background. But I often don't want it at all and will shut it down, and maybe even disable it so it won't start with MC. I've therefore programmed my remote's 'MiniLyrics On' item to start it if it's not running and otherwise bring it to the front. 'MiniLyrics Off' simply hides it. If I didn't want it running in the background, I would program that to quit. In other words, add a global hotkey for 'Quit', and use that.