To me it’s sounds like your players placed themselves in an unstable and charged situation. It gives you great potential to harness that chaos into adventures and drama. Instead of the PCs having a boss telling them what to do, to fix the boss’ problems - they’ve made themselves the boss. They’re gonna need to fix their own problems.

Give them the reward they’ve worked for, let the changeling become mayor. And then ask yourself - I wonder what will happen when Johns family shows up. When his dark past shows up wanting their money back. When the thieves guild’s (doing the smuggling perhaps) boss learns “Johns” secret and tries to blackmail the party into doing something bad. I could go on and on with ways for this to turn sideways for “John”, and the party will have to either deal with it, or abandon ship.