From the article:

"Being effective in a company also means working hard, being reliable, and being an excellent member of the team."

Translation: keep your head down, don't rock the boat and don't have any passion for what you do. This is the recipe for 'success' (i.e. continued employment) at big companies.

"As a result, a company needs lots of smart, super engaged employees who can identify its particular weaknesses and help it improve them. However, sometimes really smart employees develop agendas other than improving the company."

No. These so called 'agendas' don't just mysteriously appear. What happens is that the big company goes to great lengths to hire smart people, and then even greater lengths to ignore them. At this point, the smart employee has two options (1) stay or (2) leave.

From sarahmccrum's comment in this thread: "I saw that most of the clever people who were around left, often when they were most needed"

That's the second scenario, the smart person says "screw it" and leaves. Sometimes that is the most mature decision. If some behaviour that is bad for the company is deeply engrained, is it really worth the futile tilting at windmills quest to get it changed? Perhaps they have gone on such crusades before only to get burnt (at the stake).

In the first scenario, where they stay, what are they going to do? They can (a) decide to ignore the thing that is bad for the company, (b) decide to keep banging their head against the wall in the same way, (c) escalate - by trying to change the way that they communicate the seriousness of the problem or the audience (brass didn't listen, maybe the grass(roots) will?).

(a) shows low levels of motivation or commitment to the company (but hey, apparently that is a good thing so long as you hide it (sarcasm)), additionally, it can be genuinely difficult for smart people to ignore situations that are sub-optimal. If you're a programmer and your job basically boils down to 'fix things' ... it is very hard to draw the line and not try to fix a broken process. It is that itch that needs to be scratched.

(b) is just going to continue to get them ignored, or perhaps labelled as 'not a team player'. Way to go corporate culture. Eventually they'll get fired or tired and switch to a different strategy.

(c) is the 'problem'. Smart people aren't always good sales people. And it is fundamentally a sales problem, where they need to identify the right people to make the change, and then sell them on the idea (by convincing them they will save money, and that it was their idea in the first place). Now the geeks with low social skills is a common cliché, lets ignore that tired and played out meme...

...consider if you will the problem of identifying exactly who the people are to get on board with the change. Power flows in strange ways in big companies, it isn't always just a linear thing directly from the top to the bottom. In my experience it is almost never linear.

Identifying the true power structure in a corporation (for a particular change that is required) is enormously difficult. Moreover, the underlying power structure can change depending on what the problem is, or over time, or any of many different variables can effect what the true power structure is on day X for problem Y. Becoming a better communicator is practically trivial compared to the problem of identifying the correct power structure to address the problem.

So you might think the moral of the story is that geeks need to become better communicators. But NO! Certainly not! Becoming a better communicator is the path to either management or architecture, neither of which is a fate that I would wish on anybody.

For the smart person stuck in a stupid situation, the smart thing is just to move on. It doesn't matter that you are not loyal to the company, you gave it a good shot. Try to leave on good terms (itself a marketing problem (blah blah professional development etc)). Loyalty doesn't matter, because the company has zero loyalty to you. And true loyalty must be bi-directional.