I agree that if the disease luck had gone the other way and a large fraction of Europe had died of disease then it's possible the Native Americans would have remained unconquered. If the disease factor was just taken out of the equation completely, I think the Native Americans would have been conquered, simply because of the great European advantage in technology. But the conquest would have looked more like England's colonization of India, and many more of the native cultures would probably have had a chance to evolve and assimilate modern technology, like India's cultures did, rather than just going extinct.

There's some speculation that Syphilis may have been a new world plague. The first major outbreak was a couple of years after Columbus returned, but figuring out when the first ever case was has proven more difficult.