Would you use a website if it messed with your mousing speed or your cursor? You would you grind your teeth. I feel similarly about non-native scrolling.
The only exception I will grant is for people developing fling scrolling for webapps on the iPhone and iPad, because that is carefully tuned to mimic one operating system on one kind of device. Anything for more general web browsers, however, can make no assumptions and should leave my scrolling alone.
Bottom line is that the scrolling is beautiful and works well, why would users not like it?
You won't be able emulate scrolling fully until there is a standard for mousewheel events that includes full X/Y delta information instead of uniform discrete steps. I haven't seen any plans for this in HTML5 or elsewhere. And at the end of the day, anything done via JavaScript events is just not going to match the reponsiveness of the browser scrolling the element natively; for such a fundamental operation, the cosmetic benefit of a reskinned scrollbar just does not outweigh the UI friction.