I am not sure that it is refuted as much as it is considered an artificial rendering of Ancient Greek. To provide some historical/linguistic backdrop, Ancient pronunciation rules were established centuries afterward by Desiderius Erasmus (c. 1500's C.E.). As such, there have been recently a lot questions concerning the authenticity of the Erasmian Pronunciation, whether or not his rules correctly recreate Ancient sounds (specifically Attic Greek).
A secondary issue surrounds when sounds changed in Greek. Unlike other Ancient Indo-European languages, Greek is far from dead and has a considerable spoken history. Undoubtedly, the over 2,800 year (assuming that the Homeric Poems marks the origin of written history of Greek) history led to various changes and dialects. Many contemporary scholars question when sounds actually changed from their modern ancient to modern usage. Some suggest that as early as the 1st or 2nd century C.E. the sounds changed to their modern forms; some even go farther back in time. Regardless of exact dating, it would seem that a vast majority of Greek's linguistic history has used modern pronunciation.
The third and most hotly debated is pedagogical in nature: Considering the relative disparity between Ancient Pronunciation and Modern Pronunciation, does it didactically make sense teaching the Erasmian Pronunciation of Koine and Ancient Greek? Many contemporary teachers are teaching modern Pronunciation rather than the Erasmian to help display the continuity of the Greek language as well as prepare students for practical application of Greek. This is the case at Harvard, which applies Modern Greek Pronunciation even in Ancient Greek courses.