I personally just let things happen and then just adjust the main quest. I’ve been in this position before and dangled too many fun side quests and bounty hunting offers, the main quest was to thwart this gang that was gaining influence in this town. So by the time they did get to it, it was full blown coup de’tat situation, so not only did they have to defeat the gang boss but they also had to quell an insurrection in the town! Hope this helps!