How to completely Disable Cmd + [Num] in Safari?
Using OS X 10.9.4 and Safari 7.0.5, I've replicated the results of your shortcut alteration attempt. It seems that adding the new shortcut doesn't replace the old one.

Removing everything from the Favorites Bar works for me. This is certainly not an ideal solution, but depending on how you assign value to the usefulness of the Favorites Bar and the importance of potentially lost content, this may be useful to you until a better solution is discovered. 

Extra info and opinions: 


The problem persists after hiding a non-empty Favorites Bar
I'm surprised that Apple doesn't list all keyboard shortcuts for their own applications in System Preferences