Anakin isn’t killed because George was confused over two Anakin’s.
Which was never the case to begin with, anyway. In fact, while George did say that people were going to be confused by the fact that there were two Anakins as main protagonists, he never instructed the authors to kill off Anakin Solo. He only stated that Anakin should not have been the main protagonist of the New Jedi Order series, and suggested that Jacen should have taken that role instead. The authors made the decision to kill off Anakin on their own; no one directed them to do so. They could have easily kept Anakin as a secondary character without killing him.