Shimmer, I've had to be very cautious in choosing a T for this very reason, as well as some others. Because the Christian worldview is so intrinsically interwoven with the innermost thoughts and intentions of people's hearts, it makes conversations about PD-related things and my personal recovery really dicey with a non-Christian T. (And even on OOTF, most days.)
I believe that EMDR and treatments for PTSD/C-PTSD have a lot to offer individuals. Psychology is only just in its infancy in beginning to delve into the workings of the brain, though, and will understandably leave spiritual beliefs out of the equation in the pursuit of unbiased science of the brain. What stands is that much is still theory -- and theory that your therapist may hold to with a very firm grasp over any spiritual worldview. So, that remark is understandable from her side of things.
My encouragement would be, in light of this, to acknowledge the stumbling block if you are already struggling in your faith and get into an environment where your faith can be built up for a season. Think Christian therapist or biblical counselor. Get to the root of some of these issues as far as sin/pain/the fall are concerned, start allowing Jesus to work in that pain in the way He needs to, then see if it would be worthwhile to return to the other T for EMDR or any other treatments for trauma that a secular psychologist may be more well-versed in. (You make luck out and find a Christian T that does both. I have not found them to be wholly nonexistent!)
Blessings and God's grace to you as you weigh your decisions.