Just a thought: I believe the 'thermo-couple' controls all gas flow, including the pilot, so it should be ok.I'm not sure how the main burner supply is controlled, but think it is fed via a solenoid valve (possibly 12V but more likely from the Thermocouple) with the circuit guarded by a 'High Limit' switch.
If your fan was failing, the high limit switch may have tripped and need resetting .
Note: I'm not familiar with your particular
furnace but this is the concept with household gas furnaces: If you lose power (for fan) and there is a call for heat, the main burner will light, overheat the system, trip the 'safety', and prevent fire. But, the 'pilot' will stay on.