Which is the less bad option for a 12-year-old with GERD? Long term PPI or fundoplication? Vomiting returns when goes off PPI.

Hard to say. Gerd is a variable process and treatment includes dietary, behavioral, medication and surgical approaches. I don't know anyone who would operate on a kid that age that could be managed well by PPI's. That decision is better made by those who have more data on the past treatment and present status.