Moral?
What I took from the film is people say things like "I wish I could just erase them" everyday. This movie provided a scenario where people could have pieces of their memory erased, but each person seemed slightly empty after the procedure. Joel, Clem, and Mary all gravitate back to what they originally erased. And Mary sending all the patient files back to the patients, maybe because she felt they were "missing" something too. To me it seems like these memories are essential to the people they have become, and they are meant to be a part of you.
Also it's strange to me that people don't like Joel and Clem together. Sure one is more outgoing and sure you see the fight, but isn't that what's realistic about the relationship.? Idk, I just really love them together lol.