For anyone else coming across this by search.. There is at least a workaround: in System Preferences > Keyboard Shortcuts > App Shortcuts, add a shortcut for Evernote.app with the Menu Title "Delete Note" and whatever shortcut you prefer other than Cmd-Delete.
This will replace the Evernote shortcut, so Cmd-Delete will no longer delete notes. As a bonus, your new shortcut will now work within the note editor, as well as the note list and search bar.