It's not a religion if you can measure your God scientifically, so there never was a religious undertone in DS9.
That's begging the question.
The Bajorans believed in the Prophets even before they knew about "wormhole aliens", or even wormholes themselves. So the "Prophets" remain religious figures even after the Federation comes along.
A Bajoran would likely respond to you that "your science simply proves conclusively that our Gods actually do exist".