I don't know what Amaral thought, and neither do you. I know what he said and if he was lying as has been implied that can't be proved imo.
It seems he made the correct decision to resign when the Portuguese judges ruled that his freedom of expression was not restricted, as it would have been had he stayed in his job.
He states quite clearly that his gripe was because he "responds to the need I felt to defend myself, having been discredited by the institution for which I worked for more than twenty-six years, without being given any chance to explain myself, publicly or within the institution itself."
His wife wrote of the ignominy of his last day at work when apparently no-one spoke to him.
To cap it all the tax guys caught up with his bad debt and helped themselves to a chunk of his pension until the debt was cleared.
Did it never occur to you that it might have been preferable for Amaral to resign and be able to claim the residue of his pension he was entitled to retain from the tax guys rather than gamble on perhaps losing it all if his forthcoming torture trial went badly for him.
Which in the event was rather prescient of him.