I lost my father last year. The fact that he too was an athiest somehow made it easier than if he'd been expecting a quick trip to the afterlife. I remember a few months before he died, looking at some Hubble photos with him and discussing how being - in a very literal sense - a part of all this was far more impressive than religion.
Of course, it was agonising to watch him die, and to try and get used to him being gone. It's affected me in lots of ways. But I refuse to believe that there'd be any comfort in religion at this point beyond the superficial. In my experience, mourning Christians seem even more heartbroken and tearful than mourning atheists - their faith does surprisingly little to insulate them against the reality of death, when that reality is staring them in the face, and what's more they lack the perspective to accept it on its own terms. The real burden for the atheist is, as the OP noted, knowing that you'll never see them again (unless there are some serious developments in the multiverse theory).
Although my mother is very much an agnostic rather than an atheist, we agreed that religion should be kept well out of the funeral. His friends and family assembled at the crematorium, and I gave a short and entirely woo-free eulogy, before we all went off for a drink at his bowls club. It was understated and dignified and nobody had to pretend - those who wanted to pray silently were free to do so. I think he'd have been satisfied with it.
Worst thing was the clownish undertaker, impressed by my speech, pestering me endlessly to become a humanist minister. "150 pounds a service, and sometimes you do two in one day!" Not something that especially appeals to me, but certainly not while I'm still at my own father's funeral. Other than that, it was relatively easy to bear.
As slingblade said, it's surprising how easily you find yourself having imaginary conversations with the people you've lost. I still occasionally talk to my dad now. I don't think about it too hard - part of me is thinking "well, you never know", but mostly I'm fully aware that I'm just comforting myself. But it seems an appropriate way of remembering someone, given them space in your head to slowly fade away, rather than being ripped suddenly from this mortal coil (and however it happens, it's always sudden).
Really, the advantage of atheism when dealing with the death of a parent is that it toughens you up. You're able to deal with it as a man (or a grown woman), rather than a crying baby trying to communicate with the invisible ultra-daddy, who just folds his arms and looks the other way, however hysterical you might get. I feel like I've grown up a lot, emotionally, and I'm not sure that would have happened if I'd had religious faith. And really, overseeing your emotional growth is part of what fathers are for, and part of what makes them proud. As a parting gift, it's harsh but fair.
