I understand how you feel. It would give me pause. I see a massage therapist who believes in a lot of pseudoscience. I just ignore the occasionally bizarre things she says because I feel great after seeing her and she gives good massages and I sense she is a good person. It doesn't affect our massage sessions.
People are complicated and not consistent. They can think logically in some areas, and not others. If your therapist has been good for you so far, and has good insights into you and your behaviors, and is empathetic and human and is teaching you new and useful stuff, then who cares about the pseudoscience? I don't see how it affects you, unless she says one day "here, hold this healing crystal pyramid," and you're like, "no thanks, I'm not into that."
I agree that this is an opportunity to practice acceptance. I mean, my therapist is deeply into a hobby that mystifies me. When I first learned of it, I was like, "Seriously, you care about that?" It made me wonder who he really was. But it's not like it affects our therapy or our caring for each other.