Isak´s dislike of religion comes from associating it with his mother´s illness.
The bible verses she sends him imply that her delusions might often be relatated to religion, which is not uncommon in real life. On top of that growing up with a mother that suffers from a psychotic disorders or something like that, might have caused him to develop fear/dislike/distrust of things that could be considered imaginary, or that have to be believed in, instead of something everyone can see. He might also have fear of inheriting her illness and subconsiously believes that by distancing himself from religion he can protect himself from going insane.
Vilde and Girl-Chris were friends before Nissen
They appear to have been in the same school before, and are already good friends when season 1 starts, which was pretty early in the first semester of their first year.
The official character profiles confirm that they went to the same school before Hartvig Nissen, namely Ruseløkka skole.