When I said DS9 broke a lot of rules of Trek what I meant was that it broke off from what Roddenberry wanted a Trek show to be and what a lot of fans may have wanted it to be. Not debating that things like religion and money didn’t exist outside the Federation as I agree with your point on that but it wasn’t coincidence that DS9 came out after Roddenberry had past.
DS9 showed a darker, more political, morality ambiguous, grittier side of Star Trek and it is always a gamble when studios/writers go in a different direction from what the established fan base is perceived to want. Like someone mentioned, the mere fact that it was set in a space station instead of a starship was already a big no no to some fans. I personally like DS9 very much but a lot of my Trek friends don’t. Am just happy my son likes it so I can enjoy with him
On a related note, I read somewhere that Voyager was supposed to be darker and grittier too but in the end the powers that be wanted a more upbeat version - as upbeat as it could be considering they were stranded!