Everyone is ignoring the historical problems here. The movie/comic separation is pretty small compared to the DECADES of time that came between them. The aliens and psychics were far more appropriate when it was published (the psychics especially as both military superpowers were popularly known to be looking into "psychics").
While narratively I prefer the movie ending, I still prefer the comic ending over it for one simple reason: the movie ending completely ruined what was, to me, the most important character in the entire thing. Forcing Doc's hand completely ruined his voluntary exile. While in the comic we were watching his apotheosis into a god as he came to terms with what he had become and began to give up on the humanity he no longer possessed, in the film he's just a superhero who gets tricked into leaving. The Doctor Manhattan in the comic wouldn't have even bothered dealing with such petty concerns.
Additionally, the comic's ending was sort of an "oh" ending. It ended abruptly, not entirely satisfactorily, and somewhat strangely. However, such an ending was PERFECT given the rest of the story and the themes of the comic. The nice and tidy ending of the film ruined that for me as well.