I doubt it. However, with 1.2 they can now upgrade the temple to the appropriate one of their own type when the next city type is reached (I don't think we could do that before...but I might be wrong.) I don't think I've ever seen evidence of the AI destroying a foreign temple.
On rare instances where I have lost and recovered a province, my temple is always still there. I seem to see the same when I come in conquering provinces that have changed hands before I arrived: foreign temples.
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