Obviously, they don't prefer them in that sense.
But if the derailments are <X% of the trains, and the rest of the trains are more cost-effective enough to make up for those, especially if the costs of the derailment to the environment, communities, and employees and such are externalized away from the MBA making these decisions, then they may decide it is worthwhile.
This is one of the reasons so many people have varying levels of distaste aimed at "MBAs"... it's not that hard to train people to push numbers around in any number of industries. It's easy to equip somebody with an MBA capable of doing that. Heck, based on what I've seen of MBA training, it's trivial compared to an engineering degree, no offense particularly intended, but it really isn't that hard to tell whether this number is bigger than that number, even with some statistics thrown in. The problem is that there is no way to scale up understanding all the details that are not and perhaps even can not be in the numbers, and that's where the MBAs can go trampling over companies.
I'm sure the numbers on these jumbo trains look great, even accounting for the derailments. I'm sure of that because the fact they're running them is pretty much proof of that. If the numbers weren't good, they never would have become popular enough to be worth writing about in the first place. The question is, what about the things not in the numbers? That I can't speak to and must defer to people with experience in the industry. So must the MBAs, but they are trained, deliberately or otherwise, not to.