I think the real problem lies with the lack of resolution of certain conflicts at the end of the story. Earlier in the story line, the author states through a character that 'much more is at stake' than the fate of Meg's father, who is finally found and set free from captivity on the planet of Camazotz.
If Mr Murry is indeed rescued and restored to his family in the 'happy end,' things are NOT resolved on Camazotz or elsewhere, are they? What happens to the little boy punished for bouncing his ball differently? To the other inhabitants of Camazotz? The author does not say. Unlike what is suggested earlier, the order which is restored in the Murry household on Earth is only a tiny bit of regained territory when it comes to the malign influence of IT throughout the universe. Meg's problems and those of her family are solved; her universe is 'fixed' but not the universe in a global way.
Remember, though, that 'A Wrinkle in Time' is after all a children's book written for a child's mind-frame, and for children the word 'universe' is too abstract a thing to understand. A child's 'universe' starts and stops within his or her own realm of experience in this 'age of innocence.' In this context (and this context only) the conflict of the story is resolved.
Surprised? - no. Disappointed? - yes. As a novel that pits good against evil at every turn, the overly happy ending suggests that all evil can be overcome, complete with joyous reunions. For me, this is too sunny of an outlook - granted, I prefer novels where main characters die and rays of potential hope are apparent without slapping you in the face.
I think the sunny-side up ending to WIT makes it a good novel for adolescent readers who still need the happy endings. It doesn't provide for a very thought provoking final discussion, though, outside of whether or not it should have a happy ending. Is my cynicism showing yet?
By concentrating on her love for Charles Wallace, she is able to restore him to his true identity. Meg releases Charles from IT's clutches and tessers with him through time and space, landing in her twin brothers' vegetable garden on Earth, where her father and Calvin stand waiting. The family joyously reunites, and the Mrs. W's visit the happy scene en route to further travels.
You may be disappointed in the predictable triumph of good vs. evil, but I was not surprised by the ending. It is all in Meg's realization that her strong ability to love is a powerful weapon.