Matt,
You make a good distinction.
I am usually armed at church. This is because I carry everywhere I go. I don't specifically carry "TO" church; but I do carry, and go to church. I'm not armed against religious persecution, but I am armed -- and I suppose religious persecution could be the cause for someone shooting up a sanctuary. Or, as you say, he could just be after the money in the offering plate.
If someone tries to harm others while I have the means to defend those others, I will do my best to prevent it. If someone tries to harm me, I will do my best to defend my own life. This is true regardless of where I am when it happens, whether at church or elsewhere. If I have the means to prevent evil, and don't at least try to do so, then I believe the blood of the victims would be on my own hands as well as on those of the murderer.
My conscience is bound to protect myself and my family, so I carry the tools to do so. Other Christians might find themselves bound to accept whatever happens to them, and unable to carry a gun at all, or unable to carry a gun at church -- and be just as right in the eyes of God. Regardless of what beliefs others may have, I am bound to do what my conscience requires of me, and I will do it.
Frankly, I'm not sure how I'd tell the motives of the Bad Guys at the moment something happened. I'm not quite callous enough to say, 'shoot 'em all, let God sort 'em out.' But I am callous enough to say that my conscience allows me to protect myself and others regardless of where I am at the time, and that God knows my heart.
And that's where I rest.
pax
Or why is my freedom judged by another man's conscience? -- the apostle Paul, in 1 Corinthians 10:29