If Chrome outright disables JavaScript's ability to alter the "Back" path, it may brake some (poorly designed) applications. A compromise is to prompt with a warning.
Break them then, with no warning. Letting Javascript trump browser controls (or spam confirmation popups) is a problem that never should have been allowed to live beyond the 90s.
But changing the behavior suddenly can make existing applications outright not function. That results in angry customers. A prompt is a decent compromise. Example prompt: "This website has altered the web address of the Back button. This can be risky. Do you want to use the application's version of the web address, or the original address? [Altered address, Original address, Cancel 'Back', More-info]"
