Guess you were lucky, like I said the issue happens only when you start a GC game the first time (after you turn on the console) and on the bios screen, if you unplug and re-insert the MCs after the game starts it works fine and seems to also work if you select another game and on the biso screen again.
btw don't you use a Wii U?
I can relate to that, Wii is my main etretainment media player, I use it to watch movies and play music too, and many times I leave it on while doing other stuff for hours, I don't remember it ever overheated on me, just as long as there's no disc spinning inside I think it's okay to leave it on for hours.