Well, as a Catholic, when my Grandmother died, the things that were most meaningful to me were that:
a) death sucks
b) I enjoyed hearing about and talking about my Grandmother.
It's true that death sucks. In the beginning, we were not created to die. Death came about as a result of original sin. It suddenly hit me when my grandmother died (as the first person I was somewhat close to who died) that it wasn't just this "part of life" that I could think about somewhat romantically, but it really really stinks. Sure, there is a glorious reward for some who die, and that is a consolation, particularly for those whose loved ones stayed faithful and close to the sacraments, but even so, it still stinks for those of us who have to experience the loss or watch the deterioration etc...
I don't know if the grief of an atheist is worse than that of a religious Catholic - after all, my atheist brother just figured my Grandmother would turn to dust like everyone else when she died, but I'm the one that was worried about the possibility of hell for her as a fallen away Catholic. People did say "she's in a better place" to me, and I found it burdensome to smile and nod all the while wondering if she might be in a worse place.
So my point is that you can just be there for your friend. She might be surprised by her emotions - maybe she could use someone to talk about them with. You don't have to tell her "he's in a better place" anyway, because unless he is canonized, you can't know that for sure. Just listening, nodding, and agreeing that death sucks is enough (even if you have a different reason for disliking death than she does). She also might want to talk about him. So ask her what he was like, give her the opportunity to talk about him. It is comforting to keep a person's memory alive by talking about them. You don't necessarily have to do all this - maybe she doesn't need or want to talk about him. Like the others said, continuing to be her friend and expressing your sorrow for her loss is a good place to start. Ultimately, she has to grieve, and who knows if this difficult loss might spark something in her.