Yeah, the entrance you went into is the one I'm referring to. I seal it up every time I enter or exit so I at least attempt to make it secret. As for the torches, there are no torches anywhere that can be seen leaking through the surface, though I have seen my own tunnel many many times when first logging in, so I'm familiar with the loading glitch. I don't know of any way to get around it except wander around in complete darkness, which wouldn't really be a problem if mobs weren't active. You can see lava and torches with the loading glitch, and i assume you can also see redstone torches and lightstone.
Hopefully by "clean up" you mean "try to get rid of the griefers."
Edit: You do, that's good.