Yeah, i'm quite positive it is Virgin Mary. Remember ayu is wearing a white wedding dress on the M PV? It represents "virginity".
There are a lot of other reasons why it is Virgin Mary she's talking about and not Mary Magdalene (check my posts on the previous threads).
Catholics, which is actually the religion that prays for saints, don't often pray for Mary magdalene THAt often either. (brazil is the biggest catholic country in the world and I've never sseem anybody here EVER praying to Mary Magdalene to be honest). They often pray a lot for Virgin Mary, which is what ayumi is doing in the beggining of the PV (praying, and then Mary[ayu, on the PV with the wedding dress] appears in her prayers and grant her some light for her contemplative thoughts).