It is not in the Calibre preferences but in the Viewer preferences. Open an ebook in the Viewer and while in the Viewer press ESC to get to the menu, then the option is under Miscellaneous.
I also checked that the destructive edit happens upon viewer close, not open or page turn.
Also the version 4 ebook viewer is step back from the old one, as it stands now. It is slower, more resource hungry and buggier. The only arguable improvement is it now uses a 'flat' theme that doesn't look dated. I'm even considering reverting back to Calibre 3 because of the ebook viewer randomly freezing on large epubs with equations and so on.