Sounds simple enough, but how do you implement it? How do you get the resources not only across the Atlantic but also across the continents fast enough to be effective? Even today, WHO would be hard pressed to handle a widespread outbreak of smallpox in a under developed country. I don't see how an early modern European state could do it.
Even with modern medicine, treatment for measles and smallpox is primarily supportive -- assisting the person to survive the symptoms while their immune system fights the cause. The American Natives' immune systems have no experience with these diseases (or even similar ones). It's not clear that any amount of supportive care could prevent a massive number of deaths.
With modern medicine, there is no smallpox.