That's not going to happen so long as they are assailed by ill-thought-out or outright abusive message boxes (e.g. Windows Messenger spam and message boxes from web pages). Programmers tend to use message boxes because they fit easily into their view of the process - "at this point I want to know what the user wants to do, so I'll ask just here" - not because they are the right UI element.
It's not just desktop users that have a problem with message boxes, anyway. They've also been a nuisance for system administrators who want to automate processes such as installing patches. Microsoft has now provided better patch management tools that allow a lot of automation, but I believe there are other sysadmin processes that can still be interrupted by message boxes.