But if she lift up her drooping head and prosper, among those that have something more then wisht her welfare
It's interesting that he sees the church as this objectively good being and idea, and that people have done damage to her, though she is still good, just downtrodden. Rather than the people being the church and their actions being representative, thus painting the church itself as bad.
hence forward be that which thine own brutish silence hath made thee.
Silence created the circumstances and destructive actions to come, and Milton is criticizing and combatting that silence by his writing of this work.
I foresee what stories I should heare within my selfe, all my life after, of discourage and reproach.
He really feels a strong obligation to write this, and a spiritual conviction, which if he doesn't follow will end in discouragement and harm to his faith and livelihood.
But when God commands to take the trumpet and blow a dolorous or a jarring blast, it lies not in mans will what he shall say, or what he shall conceal.
This is interesting. Milton believes that what he writes is not within his will to conceal, that he absolutely must convey what God has commanded, seemingly prophetically.