No matter what they and their parents believe in, lots of kids have nightmares and/or worry about stuff that they needn't worry about. Ask yourself: would you be so alarmed if the girl was having nightmares about monsters under her bed? Probably not, that sort of thing is normal with all kids no matter how their parents raise them. So, first of all, make sure that the thing unnerving you really does centre around the child worrying about stuff in general, and not simply that you don't like the things she is worrying or writing notes about.
You might be thinking that if she hadn't been told something existed, she wouldn't be scared of it - but if you search online for advice on how to stop your kids being scared of monsters at night the overwhelming majority of advice sites claim that telling kids that "monsters don't exist" doesn't work. Most advocate instead saying things like "mummy and daddy have special powers that keeps monsters away", which personally I think is rubbish and with my own kids I just stuck to the line that they don't exist, but I accept that this kind of advice probably represents a majority of cases where it hasn't worked. Really then, the beliefs of the girl's parents may be the subject of her worries but they probably are not the cause.
Actually, the note you quoted where the girl wrote "God why don't you make satan die" - although that is a little odd from a child, it is an interesting theological question! I think that if an adult was taught that God and a devil existed they would probably ask a similar question - why would a benevolent god create an evil creature and allow him to exist? Some find an answer to that question that satisfies them within religion - others may not, and it could lead them to look elsewhere outside of religion and philosophy for answers about life. It may have been questions like this that led you to be an atheist, I don't know. My point is that the things she is thinking about may be more of an "awakening" than something that is going to trouble her for life.
What you should probably do is let her parents know that she appears to be worrying about some things whilst she has been in your care. Maybe give them the notes, but don't comment on the contents of them. You could just say something like:
I thought I'd pass these on to you - [name of child] wrote them at our house, and I just thought if she was worried about something you'd know how best to deal with it.
If they are as moderate as you say, then they may well feel the same way as you do, that it isn't healthy for a 6/7 year old child to be worrying about those things, even if they do believe in them. As an analogy, many parents today feel it necessary to teach their kids about safety and how to deal with strangers, but you wouldn't want them to lay awake at night worrying about strangers, even though you know they are real. Hopefully your friends will talk to their child the best way they know how to stop her worrying.
As you want the behaviour to stop in your house so it doesn't influence your own kids, by all means monitor the situation, but you may need to allow some time. Kids don't stop believing in monsters under the bed after one pep-talk, so this may also take her parents a bit of time. If after what you consider to be a reasonable time has elapsed this is still going on, you could perhaps say something like:
Remember those notes I passed your way? I've noticed that our girls are still talking about their beliefs, and mine is starting to worry and ask me questions about the devil. I can only answer her in line with my own beliefs. You know that we respect your beliefs, I'm just concerned about our girl getting scared about things she's heard about from yours. And maybe you're just as concerned that mine is going to tell yours that there is no such thing. Is there anything we can do about that?
That tells him that you are concerned without making it all about what he believes. I think that flipping it around and pointing out that if your two girls have a theological discussion it is just as likely she'll tell his daughter what you'd said helps to balance it out and show it could be both of your concerns. See what he says, but try to find common ground, even though you have differing beliefs because all good parents want their kids to be happy and not get confused by other people's conflicting ideas.