How do you defend the integrity of your work while maintaining a cooperative and friendly rapport? Specifically, how can one work with an editor who is perhaps a bit overzealous?
While it's difficult to say without seeing the writing in question (and the editor's comments), I've tried to answer this in a general sense, assuming the editor in question is reasonable and can be approached. If you're faced with, say, a proofreader who's doing rogue line editing, you have a major disconnect and this needs to be corrected.
I would suggest communicating with an overzealous editor early and often. Make it clear that you understand what an editor can provide (if you do), and ask for clarification on what the this editor considers to be within their scope; ask why they're making changes, so you'll understand for next time. (I assume there may be a next time.) Keep in mind that they're trying to make your writing better, and you may need to spend some time understanding what "better" means to them.
From your comment on relentlessly rewriting passive voice, I'm guessing you may have a newbie editor on your hands. Passive voice is sometimes the simplest way to communicate something, and suffering through a few rounds explaining that may, in the end, end up making a better editor out of this person. (I learned that lesson at the beginning of my short freelance career. I butchered a few chapters and then had to redo my work, hat in hand.)
Have you considered the possibility that this editor is at least partially correct? Maybe they're following an internal style guide that you don't know about? Perhaps they've been told they're doctoring the book?
In summary, if you're stuck with this editor, build a relationship where you can and learn from each other. If time is limited, revert the changes, explain why you're doing it, and communicate later.
As I answered over at When editing for a person, how much can be changed?
About all I can suggest is that you learn to love (and use) the word stet.