twain alludes that when a prayer seeks victory for one side that mean that the other side will be defeated in the battle.the prayer is not creating a positive effect for neither sides.he gives the analogy of the rain which on the one side might be really beneficial but on the other hand it might destroy the farmers crop
I dont know why she wants jig to stop talking but I imagine she says it over and over again to show that she is aggrivated and to make her point to show that she wants him to stop talking.