Without second guessing or judging the pilot's thoughts and decisions in this case I can't understand why anyone landing for fuel would be quarantined. Surely the point of quarantine is to avoid the person coming into contact with in country persons. If you get back in the plane and go on to your destination you are achieving exactly that. If you are quarantined you are going to come into contact with people on the ground, drivers, hotel staff, service people etc. Rather counter productive!
In spite of the current new quarantine regs. it appears only a few small percent of arrivals are being quarantined (we are told as little as two or three percent,) and there are reports of non essential journey arrivals just walking out of YVR without inquiry as to their status.