Prevent closing of entire Xcode window on Command-W when "Quick Open" menu is open
Here's how you unset the keyboard binding for Close Tab aka ⌘+W. 


From Settings.app -> Keyboard -> Shortcuts -> App Shortcuts tap the + button
From Application dropdown select Xcode
Enter Close Tab for the Menu Title 
set any keyboard shortcut you like




This un-maps ⌘+W shortcut in Xcode app completely. After this you are free to remap the ⌘+W key bindings in Xcode.

In my case I like ⌘+W to close the document so from Xcode -> Preference -> Key Bindings I have these changes (In your case you can bind Ctrl + ⌘+W to Close Tab instead and leave Close Document unmapped).