I get that Cersei hated those religious extremists who made her parade naked in the city, but what was the point of blowing up the entire Sept? It killed lots of innocents (surrounding buildings also got destroyed). The Great Sept of Baelor building also had historic significance. And if she didn't care any of this, at least it was a total waste of precious Wildfire which could be used in wars.
She could make the faith illegal. She had access to powerful armies and royal guards which could kill all the extremists one by one. Why didn't she choose this option? Why did she go for Mad King's signature move which could spark more rebellion?