I don't have an issue like this, but I understand your sensitivity to it. It sounds like your therapist is doing what they do with any way of thinking a person has--they question it as a belief, not a fact; often, this is helpful for people to see if the way they think about something is what's holding them back. However, it doesn't work with religion, and it sounds like she overstepped herself there.

It would definitely be worth talking to her about this, or writing to her, and asking not to question your religious beliefs unless you initiate it.