Numerous flaws in this hypothetical scenario.
1) You're a pacifist, but happen to have a fully loaded gun right by you? "My god doesn't approve of killing." "THOU SHALT OWN THIS COLT .45." "... I guess he's making an exception. Thanks, god!"
2) Pacifist or not, why did you stand there and let what is apparently a homicidal lunatic round up your family? It's fight or flight, so if you see a guy with a gun, and you don't want to shoot, run.
3) This guy didn't just appear out of nowhere (but the imagining of a hypothesis). Someone saw him drive/walk up, kick down the door (pacifist or not, I lock mine) and enter what was obviously not his house. If cops aren't behind them, they will be. That indicates this is a hostage situation and he's using my family to ensure he's not in jail or perforated. I say whether you shoot the guy or not, use that gun and distract him from the swat team about to break in.
4) I can imagine a couple conditions that might make it either hit or miss, but not Kill-shot or No Shot. You're absolutely certain if you fire you're weapon he will die, instantly? Especially if the cops are there, there is always a paramedic to rush said man to the hospital. Besides, as a pacifist, once you're family is safe, wouldn't you make an effort to save this man's life? (and maybe soul - wish I knew what weird NRA-pacifist religion I was talking about. Maybe they believe in souls and candy corn as the road to heaven.)
5) This is probably the most subtle but most crucial. You aren't asking "save my family or die a martyr", you're asking whether we're more comfortable burning in hell (or whatever underworld bad people go to in this NRA-approved, deer-in-the-headlights, pacifist group) for failing to follow one tenet of the faith during a life-or-death scenario, or willing to let ourselves and those we care for die (perhaps horribly) at the hands of someone who has no idea who you are or what you believe. Burn for being disobedient or let your family die in righteousness at the hands of a heathen.
That said, shoot the loony and pray your tree-hugging god won't hold it against you.