As others have noted, there has been another arrest. The operations director was merely the first. So, the question then becomes why him first?
According to the article:
> As investigators were looking into the death of the boy, Caleb Schwab, in August 2016, Mr. Miles, then the operations director, hid or destroyed documents detailing injuries sustained by riders, the indictment said.
I'd guess that this might have something to do with it. Even if it turns out that no one did anything actually criminal in regards to the building and operation of the ride itself, destroying evidence to impede an investigation is criminal. The criminal charges for this are probably also easier to prove than the ones related to the ride itself.
Furthermore, even if it turns out there was nothing actually criminal in the operation of the ride, so that none of the owners or designers are guilty of anything, he can still go down for destroying evidence.
In short...he's potentially double screwed. So indict him first, point out that even if he gets off on the ride-related charges (which is plausible...he can try to argue that he is not an engineer, so he trusted the judgment of the engineers who designed and built the thing), they've got him on the destroying evidence thing. His only realistic hope, therefore, is to accept a deal. Tell him you really want to nail the owners and designers, and offer him a deal.