What does annie John discover when she runs home with her certificate from Sunday school? What does this experience mean to her?

I think this is when she sees her parents making love. She sees her parents in a different way. She looses her naivety about mother and father and this makes her angry.

When little Annie goes home she discovers her mother and father having sexual intercoarse. Annie sees her mothers sexuality with her father as an act of betrayal against her. She sees this as them being one person, one unit. She is particularly angered because she is forced to be her own person while her mother is one with her father.