“The problem is that the only true atonement would be to publish the original photograph, undoctored.”
I strongly disagree. The newspaper has every right to maintain their religious values, even if others think they are crazy. It is called “freedom of religion” — they have no obligation to print the picture. Their mistake was that if a picture didn’t meet their standards, they should not have published it, rather than publishing an edited version. Had there been no picture published, there would be no problem.
I fail to understand your logic that atonement for this requires them to give up on their principles. I would say their apology was pretty well expressed, and perhaps could be made stronger by expressing a commitment to refrain from doctoring photos in the future, and simply choosing to use those pictures which meet their standards in their original form.