I think that there might be a couple of ways to approach this. I don't believe that Daisy is speaking highly of Tom's intelligence. I think that she understands Tom and fully understands why Tom does what he does. Tom's depiction is fairly one-dimensional, and I believe that she understands what he is. By the same token, I think that Daisy might hold multiple dimensions in this statement. On one hand, if it is understood that Daisy grasps the full implications of what Tom is, there is a natural question as to why she cannot do anything to improve her lot. Perhaps, her statement about Tom's intelligence is a reflection about her own ignorance in terms of not being able to change such a setting or her relationship with him. In this light, Daisy might be making a statement about her own state of being in the world. This is one where she might claim Tom to be stupid, but she would be more ignorant for being with someone like him, knowing what he is and unable to do anything about it.
It surely reflects her own lack of understanding as well as self-delusion and her weak attempts to forge a genuine passion for Tom, when she has clearly had enough of his brutish ways and ignorance. Perhaps she is even being ironic and wants to make it clear that she regards him as an infant attempting to better himself.