I want to first say that there is enough lack of information in this article that it is impossible to reach any conclusion without a heaping load of reasonable doubt.
That disclaimer having been made, this sounds like a situation where the sys admin became a malcontent because he was left out of the loop on a lot of things,,,something which often happens when someone works remotely. He claims they refused to promote him to management, likely because he was working remotely and they did not think it was practical for him to manage people he never saw (they may have been wrong, but I understand why they felt that way). As for the secret meetings he alleges, I doubt they were secret. There were probably a bunch of meetings they did not mention to him because they were not directly related to his job and not worth setting up a way for him to attend remotely. Then they probably forgot to include him in some meetings they should have because A) he worked remotely and B) they had not invited him to the other meetings (the latter which there was no reason to include him in).
Having read the whole story, it reads like there was a change in administration and the new administration did not like that Williams worked remotely and was trying to find a way to get rid of him if he would not move to where he could actually come into the office (something he could not do). I think he read the writing on the wall (Sidenote: by the time the writing is on the wall, being able to read it does you no good) and wrote his letter in an attempt to intimidate them into leaving things the way they were.
My skepticism for his account of things is not because I do not think it could have happened that way. My skepticism is because the story is almost entirely from his side of things and everything still has explanations that do not require malice on the part of the Institution or its staff.