I used to work ride ops at Busch Gardens in Williamsburg, VA. There are a few reasons this may have been a problem.
1. If a CM hit the E-Stop button, I believe an evacuation becomes necessary. I think with E-Stop (Emergency stop) the SOP (standard operating procedures) requires that the ride may not be restarted while guests are on board. Some rides have an additional quick stop button which essentially does the same thing, but allows for the restart with guests on board. The main difference between the 2? E-stop shuts the show down. Quick stop shuts the ride down. That means the E-stop would turn off music/effects on a ride and probably (on this one) turn on all interior lights. Following an E-stop/evacuation the maintenance crew usually has to cycle the ride a few times with nobody on it before restarting. The evacuation of the ride would be the longest process of the whole thing. Usually you are only allowed to take between 2-4 guests at a time during an evac. If the other ride train was full, that would probably mean 7 or so trips?
2. The tracks in the loading area have something very important that I believe everyone would want to know is completely safe: brakes. That is how the ride stops. If she stepped on the track there, it is very possible that she could have hit something involving the brakes and maintenance would want to look at and test them before sending the ride along.
3. Another important thing that is located on the track there is a ride sensor. Sensors are located throughout a coaster so the computer that runs the coaster (CMs just push a button here and there, a computer does the hard work) knows where each train is at all times. Those sensors are designed to prevent two trains from being in the block (or section of the ride) at the same time. In other words, they prevent crashes. If she knocked out a sensor, or even dropped something that could block it, that could prevent a world of problems. Maintenance probably had to test the sensors to be sure they were ok.
So a couple of hours could be a real situation here. Most guests don't step on the tracks....period. Even if you see at some parks where employees cross from one side of a loading platform to another, they usually have to do it by the train when it is in station, not on the track. However, where they do it on the track, they know where they can and cannot step. Safety is of the utmost concern to a park (and most guests).
I believe all of the above could have contributed to the shut down time. I also believe the CM would have been doing exactly what he is trained to do if he hit the E-Stop button.
Incident report: those usually can be filled out while a ride is running. Usually the ride lead and maybe an area lead (at Busch Gardens, anyway) would take care of that while the other CMs run the ride like nothing unusual happened.