It's a good question. I can only assume while they didn't worship, they did have to somewhat acknowledge an existence of Nalanni. If they found out that's where the Nalawi got their gifts that made them such a threat to the Dakal, it would possibly make sense for them to try and snuff out the source to win the war. Without believing in a god themselves, they may not have considered beforehand how powerful she really was-- or how capable of mortal emotions she would be to lash out that way.

I would kill to be able to hear the Dakal side of the story and their reasoning. Nalanni sounds as if she had not interfered for hundreds of years during the actual war. She could have been unprovoked, but I don't believe it would have taken her so long to act. I think if we could get an answer to your question and why they did decide to try their luck with her, it would shed a lot of light.

Also makes sense why the older Nalawi were not cool with touching her volcano earlier.