Religious fundamentalism is basically conservative in nature. The 1920s as a decade, despite their reputation as "roaring", were also conservative. The majority of the population at that time were xenophobic (anti-foreigner), and 3 million of them were active members of the Ku Klux Klan. There were anti-immigration laws that put quotas on the number of immigrants that could come to the US, and Sacco and Vanzetti were arguably railroaded into a murder conviction that resulted in their deaths.
So the conflict that resulted was the same conflict we often find ourselves in -- agents of social change versus agents of the status quo. I'd argue that religious fundamentalists just represented the status quo of that time.
The emergence of religious fundamentalism in the 1920s might have been an unforeseen result of the growth of self expression that was intrinsic to the decade. The emphasis on individual expression of self and the changing social fabric of the time period resulted in many examples of religious fundamentalism of the time. Certainly, if there was any confusion or conflict within such an expression is came from the fact that these expressions were new to the scene and sought to modify, if not change, the overall view of religious expression. This resulted in questioning of faith and the extent of which one could believe in the self in relation to the divine.
I am not sure that it resulted in confusion. Also, I think that it is a little harsh to blame the fundamentalism for the conflict. You could just as much blame the city people...
Anyway, during the 1920s, American society was changing in a huge way. There were way more people in cities than before and their culture was changing. There were all sorts of new things to do for fun. There were flappers.
All of this looked to rural traditional people like it was an assault on American values. Historians say that this is why religious fundamentalism rose -- it was a reaction to these new ways. The rural people reacted by going back to the old ways.