First- the secretary was way out of line here in being rude to you about your family and arrangements. I'm glad you reported her and will meet with someone about it.
Next- I find "I'll pray for you" to be reasonably condescending, no matter how the speaker meant the comment. Even if I believed in god, why would you think you should intervene in what should be a very personal relationship, i.e., my life and god? If someone says this to me, I usually respond with, "No thanks, not necessary, please don't." However, I think I'm about to swap over to "What a bizarre thing to say!" I really like that!
Finally- Montessori education. A true Montessori school offers a religiously neutral environment; it is not associated with any particular religious persuasion. However, Montessori education does not have any conflict with any religion, either. In fact, schools have been sponsored by groups representing non-sectarian interests as well as by the Catholic, Jewish, Protestant, Hindu and other faiths. Unless a religious group is sponsoring this Montessori school, there really is no place for this secretary to be espousing prayer and god in her discussions with a parent.