Milton does know the dangers of what he is writing about. Many people before him have lost their ears for saying stuff against episcopacy (like, literally, they had their ears cut. I didn't imagine reading that, did I?). Regardless, Milton takes on this controversial subject because he believes it is his duty as a writer and a persuasive writer at that. I guess what Professor Burton said about Milton having friends in high places is what protected him from most of the outrage that was certainly taking place after people read these works.
In the introduction to "Of Reformation", this guy, Don M. Wolfe says that although this is at a point before Milton really got a knack of prose, it is to be read for the brilliancy of it's imagery. And as I heard at the end of the class recording, there are several passages within these works that create an image that probably got Milton into some trouble:
(especially this one, I thought)
"This is the masterpiece of a modern politician, how to qualify and mold the sufferance and subjection of the people to the length of that foot that is to tread on their necks, how rapine may serve itself with the fair and honorable pretenses of public good, how the puny law may be brought under the wardship and control of lust and will."
(And then there is this one, not much flowery language, but pretty much just puts it all out there)
"But it was episcopacy that led the good and holy men, through the temptation of the enemy and the snare of this present world, to many blameworthy and opprobrious"
(And the plan of the prelates IS REVEALED)
"And thus the people, vilified and rejected by then, give over the earnest study of virtue and godliness as a thing of greater purity than they need, and the search of divine knowledge as a mystery too high for their capacities and only for churchmen to meddle with, which is that the prelates desire--that when they have brought us back to popish blindness we might commit to their dispose the whole managing of our salvation, for they think it was never fair world with them since that time."