An interesting question. The fact that my religious solidarity with GoodK's father might make it more likely for me to alert him to GoodK's mockery than I would be to do something similar in a parallel case involving an atheist -- and this is most likely true, but largely only because our common Mormonism facilitates our friendship, while a Mormon/atheist divide would interfere with a friendship to some degree or another -- has absolutely no bearing on the question of whether my action was ethical or not.
I would regard a note to an atheist father as entirely, unproblematically ethical, just as I regard my note to GoodK's theist father as entirely, unproblematically ethical.
Mormons can't be friends with atheists? Ok.
Here's why I think you would not have alerted the atheist father, even if you were friends with him (yes, I know, highly unlikely). The fact that you and the investigator were on the same side would predispose you to be able to empathize with his/her situation, and would enable you to put his/her comments into perspective.