#8 makes a good point. I've always found that comparison and contrast essays of almost any kind are valuable. They encourage students to dig into the details of a work. A case can be made that comparison and contrast are the fundamental operations of the human mind -- that we learn about almost all things by comparing and contrasting. Any assignment that encourages analytical skills (rather than narrative and descriptive skills, which students seem to be pretty good at without much training) will be applauded by later teachers, especially those a student will encounter at college.
One good way to measure comprehension is to ask students to compare characters, actions, or themes from one text to something outside of the text. This could be other books, of course, but it might also be movies, comics, or even cartoons. I'm always amazed at the two ends of the spectrum when I ask students to do this. Students who are weak analyzers or "surface" readers generally make tenuous or overly obvious connections; those who have really understood a piece of writing are likely to amaze me with the depth of their understanding and even the complexity of their comparisons.
I always enjoy asking the question: Who do you relate with the most? The least? Why? I make sure that they use textual examples and expand on the thoughts and behaviors of the characters that they choose.
They always seem to enjoy this and it really deepens their knowledge of at least two characters in the text.
Could you ask your students to write another chapter for the book? Give them a situation and the characters that must be included in their writing, then make it their responsibility to analyze how those characters would react to the given circumstances and what they would do as a result. Your assessment would be based upon how well they do with recognizing and incorporating the style and personality of the characters into their stories.
The study of this book could actually herald a research project into the lives of spies and the dangers that they face. I should imagine there would be a lot on this in terms of allied spies in World War I and II. Coupling such research with the text could really help students empathise with some of the situations that spies faced. One possible question could be what motivates people to become spies in the first place?
How about some journal response type questions? For example: Have you ever wanted to be a spy? What do you think the advantages or disadvantages of being a spy (young or not) would be? How would you like to attend an all-girl (or all-boy) school? Why? Do you like the ending of the book? Why? If not, how would you re-write it?
You can read the summary here http://en.wikipedia.org/wiki/Only_the_Good_Spy_Young . The first thing that comes to my mind is to have your students respond to whether or not the story seems realistic. Are the characters real or do they seem fake? Do we buy the events? You can also have the students put themselves in the position of the characters. What would they do in this situation? Do they agree with the choices the characters make?