It seem like Ali did believe Rhett totally. Ali may not have met anyone who intentially lied to her before, I wonder if she'll remember this lesson, or forget it as happens often in juvenile fiction, and some other things where the characters keep forgetting the lessons they learn.
He may have thought Ali may not like him if he was just a normal kid. It's not mentioned if he had either parent in the herd, or even where Ali's mother was, as I recall. Some things about Rhett may be never said. Some of the recurring characters have actually very little information known about them, and some of the main characters, since they are not the focus character that Littlefoot is.