I have the exact same problem (at least, I THOUGHT I did). I just downloaded/installed WiiMC today too, and couldn’t exit without freezing. But, I found that if I exit from a movie/show and wait like five minutes, it eventually returns to the menu screen. So, it doesn’t seem to freeze so much as ‘take its sweet ass time.’
I have had a few occurrences where the files from my USB drive don’t show up, and all of the folders are empty, but if I hit the home button (return to the system menu) and reload, they’re there.
So, maybe you can try just waiting a little bit when you exit. It’s annoying, but it’s better than hard resetting your Wii/HDD.