BTS, Jeremiah spoke against the scribes, Jesus chastised the Pharisees over and over and the scribes.
He spoke against particular individuals and practices, PSAC. Not against the religion itself. God appointed Jeremiah to confront Judah and Jerusalem for the worship of idols and other violations of the covenant described in Deuteronomy. He never spoke against the covenant. He spoke about the scribes, priests, and kings violating the covenant. This is not the same as speaking against the covenant.
Organized religion tries to revoke personal freedom and control our personal relationship with God.
My religion does not do this to me.
The degree to which they succeed depends on the person, this is true, but the most horrific events in Christanity can be "blamed" on its Organization.
They can be blamed on false teachers, wolves among the sheep. Paul himself new these would come after their passing. This circumstance is no different than ancient Israel. We see that they had evil priests, and evil kings. Yet the institutions themselves were considered to be founded by the God of Israel. Even David would not raise his hand up against the bad king Saul, because of his anointed office.
The apostles were all proponents of being guided by the HS and not by man, it seems that the generations that followed them tended to be more controlling, probably because they felt intimidated by difference of opinion.
The Apostles all wrote and spoke against false teachings. These, are as you might call them "differences of opinion." Some misunderstood Paul's writings for example, and garnered a reproach from Peter. The Apostles founded an organization and this is what they were commanded to do by the spirit.
Have you read the Apostolic Fathers? This collection was written by those that were appointed by the Apostles, and succeeded them after their passing. It will give you more insight about how the early Church existed.
And I declare to you that you are Peter, and that upon this Rock I will build my Church, and the might of Hades shall not triumph over it.
And be sure of this: I am with you always, even to the end of the age.
BTS