That sounds really bad. So much for security. What's the point of a hardware wallet if it is just as vulnerable as a software wallet?
A hardware wallet is much more secure than a software wallet (desktop wallet).
The current attack can't be prevented. This problem is tied to the OS.
The only thing which can be modified is what you see on your desktop. This can't be prevented without directly modifying the OS.
Ledger already has a 'fix' published. The recieving address has to be confirmed on the nano s.
Everything which appears on your nano s (confirming via pressing the button) is safe to use and you can be certain this address has been created by the nano s.