Calibre doesn't destroy
anything. Nothing. Not one thing.
Your files are still right exactly where they were, and you can still do everything right exactly they way you could with them. Those files also now exist as books, whose files are somewhere else, and none of your business (that is, in calibre's private library). You can set their metadata to whatever you like. You can export them with whatever metadata you like. You can do all sorts of fun things to them -- things you do them AS BOOKS, not as files.
This is why I wrote my somewhat notorious post, as referenced in my .sig. For convenience, you can find it...
here
If you want to reject the whole idea of treating books as books, with their metadata in, well, metadata, and instead treat them solely as files, with their metadata in the filesystem (and badly at that) that is, of course, entirely your prerogative. But if you choose to do so, insulting the people who developed calibre to manage books because they don't take a step backwards and make it manage files instead is not going to endear you to the members of MobileRead.