Alex... I realize that your method wasn't that tough, but you must admit that moving them through MC all in one step is even easier. That said, I didn't even think about dealing with VOB/IFO DVD folder structures on disk, since I don't use those types of media EVER. You could probably handle even this through an "All Media" view, but you'd certainly have to be more careful. With that in mind, you gave the right advice though.
That said, for more traditional single-file MKV/AVI/MP4 files, moving them through MC via any of the many mechanisms it offers really does work fine nowadays. I use this method and the File Rename, Move, and Copy tool to move HUNDREDS of GB quite regularly. I don't think having MC crash while doing this is a serious concern, unless you have random problems with MC crashing otherwise. (And if so, that's something you should address because I certainly don't.) I've also found it to be a tiny bit faster than moving through Windows Explorer on Vista/Win7 (of course, network copy operations are still somewhat broken in Windows Explorer).