Another possible storm could be one of the ultimate meanings that Kate Chopin wanted readers to get out of this story...the difference between sex within a marriage and sex outside of a marriage.  Chopin believed that real passion was hard to maintain in a marriage and that sex outside of a marriage revealed one's true and raw passion. 

I would say there are four different storms in the story.

One is the physical storm: the rain that is pounding the country.

The second is the storm of current passion that grabs hold of them with Chopin writes " They did not heed the crashing torrents, and the roar of the elements made her laugh as she lay in his arms."A third storm was two years earlier, in Assumption, when the sexual passion first grabbed hold of them.

A fourth would be the possible clash between the married couple. Chopin writes " Bobinôt's explanations and apologies which he had been composing all along the way, died on his lips as Calixta felt him to see if he were dry, and seemed to express nothing but satisfaction at their safe return." Bobinot is afraid she'll have been upset, in other words. That storm blows past, though, because another one had already been there.