Question: How could Auto act against his directive? He's playing the top-secret order he got (never to come back to Earth) in front of the captain, yet isn't able to act against it again because things might have changed in the 700 years since the order was received. And in the face of the new evidence (the plant), doesn't that contradict the order?
Answer: One of the key points of the movie is that programming can evolve - WALL-E being the most obvious case in point. After all this time, Auto's entitled to be somewhat erratic in how he deals with things. Besides, he's still very firm on his primary directive, to prevent the return to humanity to Earth - keeping the existence of that directive a secret is rather less critical. As for the plant, that does very little to invalidate the directive. It may show that the principles underlying that directive are flawed, but Auto's not got the leeway to deal with that. The directive still stands.
Tailkinker ★