Read the FAQ:
http://calibre-ebook.com/user_manual/faq.html#id31
This comes up over and over in the forums. No you can't "disable" it, it is integral to the way Calibre works. Yes Calibre copies your books into it's own folder structure for the reasons outlined in the FAQ - disk space is cheap, live with it. If you don't want two copies, then trust Calibre to look after it's copy and manually delete yourself the copy you imported from. That's certainly what I and I imagine many if not most other Calibre users do. Then just backup your Calibre folder, so both the books and the database are safely stored away.
EDIT: Sorry dwanthy, we posted at the same time. Should have known you would handle it
