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.

Of course. So you still have to destructively edit your books before you can tell Calibre to stop destructively editing your books. Genius!

I just checked and I can open the E-Book Viewer standalone, without a book.

I also checked that the destructive edit happens upon viewer close, not open or page turn.

That behaviour was for the old viewer with version 3. The new version 4 one reverts to what GP is saying: you have to open an ebook before you can even access the settings through pressing ESC or right click.

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.