What do Giles and John plan to do about the fraction against the minister?

I'm thinking that you mean "faction" against the minister. By minister I'm also thinking you mean Reverend Parris. Rev. Parris directly and indirectly fuels this hysteria. Parris has many detractors in the community. Parris is known to be greedy, whiny and on the slimy side. Giles and John had hoped to leverage negative opinion of Parris to dismiss him and perhaps the crazy witch hunt as well. Unfortunately the town was already galvanized on becoming Puritan paranoid capital of the world.