You can change the meaning of this shortcut for
TeXShop via Apple's System Preferences.
However, this requires you to set it to some command in the existing set of commands from the menu items. The one I found least useful is
Save Source Position so the following procedure sets it to that. Perhaps if you define a
DoNothing menu item then you could set it to that, but until then this should work:
System Preferences, select
Application Shortcuts. Hit the + button
In the Applications Pull down select
TeXShop. If it is not already there, select other and locate the
TeXShop application, and select Add.
In the Menu title you enter the command you want the desired keystroke to map to. I chose
Save Source Position.
In the Keyboard Shortcut enter ⌘ ↓ and you should see now something similar to (depending on your OS):
Now selecting "Command-down" ⌘ ↓
Save Source Position, which will leave you where you were.