Number the Stars by Lois Lowry might be helpful.
Another thought: when you say Clara helps kill Nazis who come too close, I would tread very lightly. Helping to set a trap is one thing, but something closer to the act like tying someone up so he can be shot is another. I don't know from your post how involved she was, but children lack the big-picture perspective to help them understand such complicated morality. If you can, avoid Clara's part in helping with the killings. Although children can handle a horror filled setting such as you're writing, they usually identify with the MC, and seeing that MC involved in killing could be very disturbing for them. It'd be like seeing themselves doing the same thing.
eta: Sorry, it should be Clare, not Clara.
I agree with this. I really love the historical fiction plot about farmers protecting the Mona Lisa, and yes there are going to definitely be darker themes whenever you set a story within wartime. While some of the older targets in the MG age range might more understand, since some of the youngest readers include 8 year olds, you might want to be careful
how you work some of those themes in.
Number the Stars by Lois Lowry is a good suggestion, since it also is set during the same time period and deals with similar themes.
However, when dealing with scenes of death, I would also like to suggest some of these MG books:
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Where the Red Fern Grows by Wilson Rawls. It's been a while since I read this one. Even so, I remember reading this particularly startling scene in 5th grade: There was a cruel kid in the story that the readers hated. He was coming at the protagonist's dog with an axe. However, while running with the axe, he trips and ends up stabbing and killing himself. Even though you REALLY didn't like this kid, his death was impactful and left the reader with mixed feelings. Though it was a terrifying and startling scene that left the reader conflicted over kid's death, in the end it was the character's own cruel actions that led to his death.
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The Shadow Children series by Margaret Peterson Haddix. This series is pretty dark overall. It's about a dystopian world where 3rd children have become illegal in order to control overpopulation. As such, having more than 2 children is punishable, and 3rd children are rounded up if found. So there are lots of themes about death (since the protagonists are all illegal children). The author delves really well into the psychological state of the young people who are not only escaping death, but going undercover and even disguising themselves as young soldiers.
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Wings of Fire series by Tui Sutherland. This is a fantasy MG series about dragon protagonists, so it might not be your genre of preference, but in the first book, the protagonist both witnesses a beheading and later his friend (the protagonist of the 2nd book) is forced to kill someone out of necessity to survive. It shows their conflicting emotions about killing, and in the 2nd book it's explored more through the point of view of the friend who struggles with the fact they killed someone, even knowing they had to.
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The Wondla trilogy by Tony DiTerlizzi. This is trilogy, but I haven't read the 3rd book yet. Again, this is more of a fantasy / sci-fi. Still, in the 1st and 2nd books, there are scenes of death (including the deaths of those close to the protagonist), killing, and the shocking nature of it. The protagonist is also put in the same position where she must kill to survive by use of traps and such.
These are some good books that handle themes about death in MG novels. They might be worth a read if you're wanting examples of how other authors approached the subject.