I don't think it was a conspiracy between church and state... it was more like the civil authorities indulged the ecclesiastical authorities.
Well, I agree with your implicit sentiment, that that program where pastors are being trained to keep the populace in check during big emergencies is certainly pretty scary...
But then again, I'm not against a certain amount of coordination, insofar as time and time again people through the centuries have crowded into churches asking for God to lift an epidemic, thereby spreading the disease quite efficiently.
I don't think there's necessarily a problem with an established church per se in the abstract, though it is not an American thing. I think it has not been too terrible a thing in Greece, for example.