I think it is a mistake to take the events of Donnie Darko literally, including the ending.
The main character Donnie is developing schizophrenia. The schizophrenia causes Donnie to believe he is at the center of a time-travel adventure that just might save the universe.
The movie shows how this hallucinated fantasy would unfold if it were reality. So the ending isn't intended to bring the movie to a realistic conclusion or even to make sense.
In an extra scene on the DVD, Donnie is having a conversation with his father and says, "Dad, I'm crazy."
Personally, I think part of the genius of Donnie Darko is that -- just like many real-life schizophrenics' hallucinations -- Donnie's fantasy almost starts to make sense if you strain to understand. But ultimately it only really makes sense to Donnie.