No sensible person would suggest that the parents shouldn't have been investigated. Even Gerry McCann himself said he understood that this should take place. Amaral, however, decided the day after the disappearance that the parents had to be implicated in covering up the death of the child, thus faking an abduction. He then distorted the flimsy evidence to fit this scenario to the exclusion of all else, ending up writing a book, making an appallingly bad documentary, and giving numerous interviews around Europe, emphasising the impossibility of the child being alive and therefore the futility of searching for her.
His activities have had the effect of turning people, especially in Portugal, against the McCann parents, their extended family and the friends holidaying with them, and it is self-evident that such animosity towards the McCanns has caused people (again, particularly in Portugal) to believe that the child is dead and not worth looking for. One has to wonder if some tiny morsel of evidence pointing to Madeleine's whereabouts, some vague suspicion about unusual local activity, or knowledge about someone's nefarious behaviour has not been passed on to the authorities because of the belief, engendered by an ex-senior police officer, that the child is dead, therefore pointless coming forward with such evidence or suspicion.
Amaral's behaviour in this matter has been immoral and inhumane. As Sherlock Holmes said in the post above, "That's not to say that Amaral has a right to try to persuade people not to bother looking for Madeleine, without being able to back up his thesis. And I don't think he had much of a care for the twins or anyone else in mind when he wrote the book..."