given what we know about the state of immunity of American Indians and Australian Aborigines at the moment of contact, can we construct an alternate history hypothesis of what would have happened if Europeans were to contact them “today” and then try prevent epidemics medically rather than via total quarantine? Would modern vaccines work for this purpose? Antibiotics? Anything else?
if American Indians were discovered by today's civilization, could doctors have prevented epidemics?
To a certain extent. When I was working in a project in a remote area of Amazonia where there was a possibility of encountering uncontacted tribes, I was required to get 13 different shots or other medications to make sure that I was not capable of spreading various communicable diseases. If you made sure that the first explorers into an area had been immunized, you could have cut down on a lot of mortality. Then you would have to embark on a massive campaign of immunization and other treatments for populations numbering in the millions. It would be an enormous task.
On the other hand, even today we don’t have things like influenza or malaria fully under control. These well could have decimated Native American populations despite the best efforts to control them.
Are we assuming that this time we’re not going to deliberately give the natives contaminated blankets and other things in an attempt to wipe them out via disease? Because that would probably help too.
It’s very doubtful that in the long run the old “small blanket” story really had much to do with it. Disease - mostly smallpox - had destroyed much of aboriginal civilization before the British came up with that trick.
Some vaccines use weakened versions of the virus, which can provide immunity to more than just the person immunized, e.g. Polio. These are used in some cases even where there are also dead vaccines available. In the case of the OP, this approach would presumably be used whenever possible.
ETA: on the other hand, the recent H1N1 flu shows that we really aren’t that good at stopping the spread of a virus through a community with no or little immunity.