First, is it ever appropriate to thank someone who's written a great review of your book?
Sure, but I wouldn't make a huge deal about it. A simple "thanks for the kind review--you seem to know a lot about the topic, maybe we can meet up at a conference some time and chat" would suffice.
Is there ever a good reason to respond to a review like this? I am tempted to let it be.
No. Let it go. I've NEVER read an author's response to a review that didn't come across sounding like a whiney "you didn't like me, but I'm just misunderstood" response.
Finally, when you submit your annual review packet, do you include all the reviews of your book, or just the mostly-pretty-good ones?
I put them all in. Even the bad reviews usually have something good to say.
And don't worry about big-shot reviewer. She read your book! That's great. Remember to go back to that review later and I bet you'll find it's not as harsh as you think it is now. You might even learn something from it. If not, well, understand that the big shots are just as insecure as everyone else, and some insecure academics need to push others down in an effort to make themselves taller. So if there's really no merit to her comments, feel pity, not anger! And be better than her when you're the big shot.