She didn't know whether she hated him or felt sorry for him. Eve stood before the inert form of Auto on the bridge of the Axiom, as she had several times before this, and still felt conflicted. Yes, the pilot hurt Wall-E, but could she truly blame him for it?
Directive A-113 . . . that's what the 700 year old directive was called, that Auto had followed all this time. In the past, that sort of loyalty to one's directive would have inspired admiration in Eve, but now she just sort of felt sad. In the end it only resulted in Auto being shut down and forgotten, collecting dust on an equally abandoned starliner.
Why did he follow it for so long? Was it loyalty to Shelby Forthright? The desire to keep control of the humans? Or was it the only thing he had left?
Eve didn't know the answers to those questions. Eventually she moved closer to Auto and brushed some of the dust off his casing, then turned and left, as confused as she was when she arrived.