But I see a problem in that scenario. If any car derails from the haul line, how does anyone know the root cause? Here we are weeks after the incident and no word from Disney about the details. Why has Disney remained silent on this issue? I suspect that if they were honest about what really happened, it would frighten most guests.
Therefore, in your hypothetical situation, if the individual gondola is to blame (because let's say the gondola grip is bent or broken) then your proposal to "just get those cars out of the way of the others and we can run it" makes perfect sense.
But what if other factors are involved? Let's say the haul line is defective. If you just get obstructing gondolas out of the way in order to run the rest of the gondolas, then you're putting everyone at serious risk. Or, for example, let's say one of the haul line motors is defective. Then again you would not want to restart the line.
For a system this complex I think you'd need a very experienced person to troubleshoot the root cause(s) before restarting the system. And, as in the previous incident, if you're not sure what went wrong it's better just to halt the system until you're sure it's safe to restart. And that could take many hours.