I don't know if your playing with words here, but that first description (atoms being annihilated) was what I meant by that the cancer had disappeared.
Just to add to what Dr Adequate was saying, there are immune responses present to deal with the suppression and elimination of cancer. These usually involve the production of cytotoxic chemicals which induce a controlled cell death of the cancer cells. The cells don't just spontaneously cease to exist. Although this usually occurs in the initial cancerous cells, spontaneous remission in more mature cancers, when a detectable tumour has formed, is known.
The other possibility is the x-rays damaged the cancer cells. X-rays have been used to treat cancer, and although x-rays are a much lower intensity, she did have three in quick succession.
But doesn't this example illustrate the importance of a naturalistic point of view. We don't know the details of what is involved in spontaneous remission of cancer, so what we do is look at the evidence to try and understand. This understanding may lead to new methods of treating cancer. However, by assuming it is a miracle, how do you then proceed to understand the process, or do you simply accept that it cannot be understood?