The AOS is only changing the common name at this time. However, in ornithology, these standardized common names are actually more important than the binominals, which are pretty much just a formality. For all intents and purposes they are changing the scientific names, as they are changing the names used for science.
The Bird Names for Birds websites heavily implies that changing the scientific names is their ultimate goal. This will actually cause far less disruption of literature and communication issue if it ever happens.