First, I would like to thank you for taking on this project. I, too, wanted to write a science fiction novel that had an allegory of the Watch Tower Bible & Tract Society and Jehovah's Witnesses.
Second, I would offer to proof your book. I believe I actually live relatively close to you.
Growing up as one of Jehovah's Witnesses I was and still am an advid fan of science fiction. My mother blames my father for this. She still holds it against him for taking me to see Star Wars back in 1977 when I was 3.
I found that many Jehovah's Witnesses are huge Star Trek fans. Gene Roddenberry's utopian future of humans living in peace problably strikes a chord with those hoping for a paradise earth. However, they miss the fact that Roddenberry was an aethist and his vision of the future was sans religion.
I think you chose wisely on using science fiction be the tool to deliver your message. That's how Star Trek got away with anti-war and racial harmony messages during the 1960s.
I think if you make a character that the readers adore and than have this oppressive regime who changes the rules as the go constantly harassing him, you will reach the hearts and minds of your readers.