Yes, if someone breaks into the server, and changes the code for the login process, they can get around this. But that's always true. The server is a higher priority target than a single account. If your scenario requires breaking a higher priority target than the one in question, it's not really a security hole.

Similarly, someone can compromise my account on a Linux box if they get root access. They won't know my password, but they can change my password or just replace the login program with their own. But we consider getting root access a higher target that compromising a single account.

In other words, this is begging the question.

edit: I must have responded to a different understanding.

Whoops. The protocol you described is actually secure against that, since your login passes the preimage to the server for hashing and then comparison.