using qwerty as an analogy for bad UI is going to influence answers, since changing the keyboard, for most users, would render a computer useless. for a computer manufacturer this would be financial suicide.
however, if we are not influenced too much by your analogy, and focus solely on the question, not all changes require this kind of compromise from the user. probably, more of them are not so catastrophic. for these kinds of less catastrophic innovations, i would say they should be welcome, given they follow solid, proven principles.
yes, it's a fact, even an innovation that clearly makes the user's life easier, may not work at all. on the opposite side of the coin, if enough people do the wrong thing, it ends up being the right thing. a huge example is how we always look to the top left of the screen... that's a prime piece of real estate now, but would have been pretty confusing in ancient china, when poetry read from right to left, top to bottom.
as ux designers we should be welcoming to innovation and evolution of the ux. if it's not us who create the interfaces of tomorrow, then who will? programmers?
at the very least, a ux designer should be sure that their application will be competitive with what is currently out there, whether with competitors, or with other sites that have a similar flow. once that is achieved, then i'd say this kind of innovation should be explored.
i wouldn't always agree @ben above who suggests that the change should be earth shattering. a lot of innovations are subtle, and are cumulative in the way they allow the user to more freely and subconsciously operate the application. if you look at the web, everything that is successful has taken some chance of innovation. even if that innovation is copying something that is huge and just tweaking it a bit... that's even more ballsy than pure innovation in a sense.
look around on the web, it is evolving every day, new innovations are introduced daily. it's like Darwin's natural selection in the virtual world. some things work, and some things don't. those that don't work will result in death, those that work will result in elevation of the species, and those that just copy innovation are probably generally safe, but no guaranties. so perhaps it depends on your personality type, or perhaps you are the kind of person that is more successful copying others...
there may even be a stigma with ux designers that create appealing looking interfaces but lack in ease of use. i'd even be willing to bet that most ux designers are guilty of this. so perhaps they should take @ben's advice above, and not move forward with these ideas unless they can confirm their earth-shattering-ness.