From a thread on a ds9 marathon on Reddit:
We know from what they've said, and how they act the Prophets are akin to the Q. Omnipresent, incredibly knowledgeable and extremely powerful beings. However since they had no concept of Linear time, they made mistakes, in the episode "The Reckoning" shows it.
There is a battle, between the Prophets and the Pah-wraiths coming. We don't when, where or how but its coming. The Bajorian equivalent of armageddon. The Pah-wraiths take their revenge on the Prophets for casting them out and not listening to them about the Sisko being dangerous.
It all comes down to that first contact. Sisko interferes with a people's way of life, and thus changes the course of history, and himself along with it. Sisko violated the Prime directive inadvertently by entering the wormhole. He interfered with the Prophets development (a secluded, and non-warp capable species) and in return, nearly brought down the entire Alpha quadrant because of it.
"The Prime Directive is not just a set of rules. It is a philosophy, and a very correct one. History has proven again and again that whenever mankind interferes with a less developed civilization, no matter how well intentioned that interference may be, the results are invariably disastrous." —Jean-Luc Picard, Symbiosis
Before DS9, the prime directive only concerned itself with less developed societies, but never before or since has it touched on what happens when mankind interferes with a more advanced one. DS9's entire story arc revolves around this.