Disable the Command-Backspace "Move to trash" keyboard shortcut
In System Preferences > Keyboard > Keyboard Shortcuts, add a shortcut for Preview (Move Selected PDF Document to Trash) that you are unlikely to type inadvertently, something like ^ ⌥ ⇧⌘ ⎋.
As an alternative to assigning a different (difficult) shortcut to the menu item, you can assign the Cmd-Delete combination to a harmless menu item, such as Edit » Spelling » Check Spelling as You Type.
The difference is, something harmless happens when you press your shortcut, but no matter what unlikely combination of keys you press, it will never perform the delete operation.
Additionally, the answer with the difficult shortcut only works for the specific PDF menu item variant, not on all variants of the item (e.g. Move Selected Image to Trash). It depends on which behavior you prefer.
The problem is: It's not possible to type Delete/Backspace in the dialog where you assign custom shortcuts. You need to do this via the command line in /Applications/Utilities/Terminal.app:
defaults write com.apple.Preview NSUserKeyEquivalents -dict-add "Check Spelling as You Type" "@\U0008"
The result:
Many thanks to @Arjan for his collaboration on this completely revised answer.