The McCanns were nothing to Gonçalo Amaral but suspects, in my view he had no personal animosity towards them until they attacked him legally in the courts. I guarantee the animosity went through the roof after that.
He wouldn't have risen to the level he did in the PJ unless he was a capable officer. He certainly had a number of high profile convictions under his belt by the time the McCann case came along.
You could say the McCann case destroyed his career.
My opinion ~ Amaral has evidenced his his animus towards the McCanns by his incapability of mentioning their names without traducing them in the process.
One addition to Amaral's high profile conviction rate - the Cipriano case, for which he was eventually awarded a criminal conviction for perjury - could explain his visceral hatred of the McCanns. They thwarted the tried and tested methods demonstrated by him and Cristovao when dealing with investigation of missing children cases.
Both were thugs who needed no assistance from anyone in destroying their careers as they and their associates managed to do that perfectly well on their own.