What about setting --clean as default behavior? I would guess that this will not cause problems. If the problem is that rm -rf is called before it could be done in more intelligent way like remove only new files and restore the rest, see bug 961623.
Why do this? What will get better? I need some arguments for the change. --clean is not safe to call universally, and I do not want to make it "safer" because it is complicated enough already. That's my argument for not doing it.
I think that it is just obvious. When I did not know about --clean option I assumed that it is the default so a lot of my tests does not use it which is sometimes wrong. But I must agree that from backward compatibility point of view it is not very safe.
Not backward compatible, I'm not convinced to do it.