This was not easy because of the way wealth and power were distributed and held by church and monarchies, and since church and state were not separate and both held power and armies, this alliance was hard to overcome when it decided to destroy a "heretical" group, a powerful outspoken person, or a wealthy group. Ultimately, even the Knights Templar did not survive it because they amassed so much wealth that they became the bankers for church and monarchs, who eventually decided it was easier to destroy the KT than to pay the debts.
The same almost happened with the Medicis and Florence, which was ultimately saved by a member of a French secret society, probably Rosicrucian but it's hard to tell.
You're right when you say that secret societies have morphed over time and are not now what they were designed to be originally. In fact, I would say that they're just the opposite. Instead of being secret protectors of enlightenment, free thinking, learning, and a more just society, they are bastions of rightwing conservatism and a very unequal distribution of wealth in the hands of their own members, much of which is disguised by "charity." Sad.