Not sure why you're blaming her for being exceptional.
It's fine if you don't want to. But becoming invaluable is not a failure on her part.
Throughout history, humanity only advanced because someone did something exceptional. And in this case, her work had brought profit for the company.
Of course it's still a mistake to make one person be the single pillar that managed the system, but it's the company's mistake.
In the first place, it was the lack of personnel that pushed her to automate the system. And upon learning she was the only person maintaining the system, the company should have spent some resources to make several more people be familiar with the system, thus making her less invaluable. After that, she can be assigned to a new project, for example.
Personally I don't like doing above and beyond. But it doesn't mean it's wrong to do so.
Being exceptional is never an issue. Being indispensable/invaluable
is.
This is the same reason the mongol empire fell. It is the same reason companies crash and burn when key personnel leaves (or is sick or dies). and so on and so forth.
It is part of your job to identify when you are clearly being relied on too heavily, and notify your higher-ups (it is even more-so part of their job, but your job includes not
ignoring it if you notice first) of this fact so they can ensure some redundancy (be that in the form of a person, or simply in the form of compiling documentation and manuals and training material for if you
do collapse). Same reason why you tell companies if you know you are going to leave them in a couple months, so they can hire someone you can train.
Just as how it is your job to tell higher-ups when they are creating an unsafe workplace environment if you notice it before them. Or that you are given too much work and risk burning out or run out of overtime. (again, even more-so their job, but also part of yours to not keep silent).
Add to that how it seems like she was in a
semi-managerial position for her department from how I understood it, it is
absolutely her job to flag to higher-ups that her department lacks redundancy and has critical points of failure.