Jefferson said that Grace’s mother died because of him, somehow in connection with Wonderland. The way he said it, I immediately assumed Alice was her mother. It may or may not be true. And she may or may not really be dead. I don’t think her being a child in the original story means she couldn’t have grown up and married the Hatter and had his child. I also don’t think that him becoming mad after his wife died proves that he hasn’t met Alice yet. Nothing can be proven based on the original stories after all, because they take so much license with them. However, they are guides for the show. And it’s entirely possible that he truly hasn’t met Alice yet.
While watching I also had another thought–that Alice might have eventually become the Queen of Hearts somehow. That’s just a throw away idea though. I don’t see how it could’ve happened.