YES!
Just what from little you wrote about your story, I think it's a really creative way to incorporate your religion and your beliefs-- using dragon tropes to represent anti-Semitic stereotypes; that's really cool~. If nothing else, you have a really neat idea on your hands, and I say shame on anyone who can't appreciate it for what it is and how much it means to you.
Of course, I can understand where your concern comes from...in a lot of fiction, especially YA fiction, whether it's novels or movies or video games, religion = evil. Religious people usually just want to control others and/or punish them; even villains who have no religious ideas can be given religious motifs/designs to hammer home the point that they are bad people...because that's how ingrained the idea is. =/
And I think it's really...sad. I'm not gonna deny all the harm religious people have done throughout the ages, but that doesn't mean the very idea of religion is inherently harmful. And it doesn't mean people with a close connection to their own religions have 'ulterior motives' when they decide to write about them positively in fiction.
I've been working on a story kind of like yours for a while now: a story where my own relationship with the religion I was raised with is abstracted into a fantasy story. ^^ And although the parallels aren't as deep as yours, I still get those concerns about 'alienating' people when I write a really positive, kind moment for the characters where they incorporate their beliefs into their dialogue...as many religious people actually do.
It feels 'wrong'; like it's not allowed...like I'm working for Disney or something and I need to tone things down and keep them secular to please the corporate sponsors. ^^; Even though in my heart, I know there's nothing actually immoral about it, I've consumed enough fiction to know that it's the opposite of what's usually done, and it still feels icky.
But I think there's nothing you can do except ignore those feelings...and the people who will eventually come to you and echo them. I mean, if it's ever to become normal to write non-evil things about religion in fiction, someone has to be brave enough to actually do it.