I haven't looked at the code, but I suspect they're just using display:none to hide elements. There's no reason you couldn't use an array as a stack so that you could keep track of the identifiers for the elements that have been hidden and then allow an undo mechanism. For elements without an id you'd add something of your own, probably a cssclass. An undo system is not too difficult to implement.
Though the one thing I kinda wish it had is an undo button -- if I accidentally remove something when I don't really want to, I'd like to not have to reload the page and click in all of the areas again (except the last one, of course).
I guess that would mean keeping track of what the last div/span/whatever you removed was, which I guess might be a little too involved for a bookmarklet. I wouldn't know -- I'm no JavaScript wizard.