This is idiotic. You use an expert tool (from a third party!) that you don't know how to use, and when you make an error you complain that it's the fault of the platform and the default interface, and that this is a trap for the unwary novice.
Your argument is nonsense. A novice user would not use Cocktail in the first place, nor would a novice even think of unhiding and trashing hidden system folders.
The default interface is fine. Why do you think the /usr directory is hidden in the first place? Precisely so that novice users don't delete it by accident.
When you use a tool like Cocktail, you're voluntarily throwing off the restrictions of the factory-standard UI in order to do what you will and run your own risks. If you don't have the knowledge to use the tool safely, you have no one but yourself to blame.
And They Said the Mac Was Intuitive