This article is idiotic if the main reason for cancelling the game is actually some "global spread" of Zika. Rio is not some city in the middle of nowhere from which no flights are coming in and out of, and now suddenly this massive international influx of visitors will come in -- it is a world-class city, a financial hub of the largest country in the continent. If we take London 2012 as a benchmark, estimates there…
I would expect the differences you mention to result in a higher delta for Rio, they would contribute to a lower base rate of travel making the event travel relatively larger.
Nevertheless, the 500,000 figure cited would represent a ~25% bump in the number of visitors (if we use 2012 figures). If you consider the area in Brazil most affected by Zika (which would include São Paulo), then this drops to 10%. You then also have to realize that a lot of those visitors displaced people who did not travel to Rio because of the olympics, which is an effect that is widely documented. Taken into account, I think it is plausible to suggest that the real impact of travel that we'd be seeing would be in the low teens or single digits.
But I think it is certainly debatable, and I guess this is the only point I really wanted to make in my comment -- that THIS is really the focus if you wanted to argue that the games ought to be suspended, but that the article doesn't address it in the least.