There are actually unused lines of dialogue in the game relating to Quelaag which imply that she may have been planned to be an optional boss at some point during development, much like Priscilla.
The following lines exist as sound files in the game data, and you can listen to them here.
Go back. Forbidden be, these parts. The realm of the creatures of chaos. They accept their banished fate.
Go back. Lest the flames devour all, and the children of chaos feed upon your charred ashes. Those who defy the pact… Those who trespass Quelaag's domain… May you feel the depth of our wrath!
Ahh, a precious new sacrifice! Forbidden be, these parts. The realm of the creatures of chaos.
Go on, go on ahead…
Welcome, bringer of meat. The children of chaos are hungry; give yourself to Quelaag's flame!
Keep in mind that speaker of these lines can't be confirmed as the lines only exist as sound files, but they seem to show that more of a story was planned for Quelaag and the chaos covenant, which didn't make it into the game for unknown reasons.
It's would make sense if Quelaag being a non-hostile NPC was cut due to development constraints, as much of the areas between Quelaag and the Bed of Chaos, including the Bed of Chaos itself, show signs of being unfinished compared to other parts of the game.