What was it that happened to the 'innocent' friends that was so dreadful? Was it the fact that they were questioned as witnesses or designated arguidos?
Why shouldn't the police question parents in a missing child case?
There is nothing wrong in questioning the parents in depth - and right at the beginning so that they could be ruled in or out.
Maybe if Amaral had actually met the McCanns and spoken to them himself, he would have been in a better position to judge/assess them. Why he didn't do that is incomprehensible to me.
IMO the attempted trial by media - based on leaks from the PJ was a disgraceful way to treat them, and showed a cynical contempt by the PJ for their own secrecy laws - which they simply used as weapon, knowing that the McCanns had no way of rebutting the dreadful allegations being made.
Also I've no doubt that finding out that Amaral was an arguido himself, suspected of being involved in the torture of a defenceless woman, in his last (and only) missing child case - hardly inspired either the McCanns or their friends to have confidence in him. Quite the opposite in fact. And who could blame them?
He should never have been let near the case. imo.