There’s almost always some complicating factor we don’t know about in cases like this: I would bet that blackmail was involved, he tried to cover it up, and the board felt they couldn’t trust him as a result of the cover-up. Because you’re right; most companies would just include the lower level employee in a round of layoffs and pay them a couple years salary to stay quiet about it all.
I feel companies are getting a #MeToo pass in cases like this: Wall Street hasn’t been holding companies responsible for the bad personal behavior of execs if those companies address the issues proactively. Investors are only punishing them if the problems are representative of the overall culture; and in this case that does not seem to be the case.
But I’m almost certain that he wouldn’t have been fired without lying to the board in a coverup. Violating fraternization policies usually isn’t a firable offense — a CEO only gets fired when the board of directors loses the ability to trust them.