Well, first off one has to wonder whether even a 3000-year baseline can truly be written off as "gradual," given the time scales involved. To be perfectly honest, the article really doesn't answer the question of whether the theory of evolution has been tested, especially in the Macro sense.
All we see is a story about how they've observed "genetic changes," but we are not told their extent. We are not told if the observed changes are equivalent to the formation of races, or to the formation of entirely new, island-specific species of bird. The article's silence on the matter leads me to conclude that the differences are racial at best.
Also, what I read here tells us only about the effects of natural genetic drift and mutation for birds residing in places where conditions are probably pretty nearly identical from one island to the next. In other words, if this is evidence, it's evidence of micro-evolution.
It is not a test of the macro side of the theory, whereby entirely different kinds of animals are supposed to evolve in response to environmental pressures of one kind or another.