It's an interesting legal issue, as she (unintentionally, it seems) created a derivative work without the owners permission, whereas the goal of art restoration experts is to try their best NOT to create derivative art-works! The fact she didn't have permission probably doesn't matter, as long as the work is "different enough" to contain sufficient originality to stand as separate from the original (and it DOES do that, lol!).
While the Church owns the painting, the question of who owns the image she created is important, as it's worth possibly millions in licensing fees for ad agencies, etc. And by charging admission, the Church is actually offsetting the costs of restoration (which she bears some liability for), if they ever decided to kill the goose that laid the golden eggs.
It's an interesting legal question, and one sure to be discussed on legal IP forums for quite some time (the gift meme that keeps on giving)...