Do you see the parent's opinion on stranger abduction as a theory? I think they presented it very much as a fact. It was very quickly being reported as a fact by the media too. Pointing out that there was no evidence to support this 'fact' was a natural response imo.
Based on what the parents are said to have found upon entering the apartment (with the window and shutters being open), to them, an abduction would seem the only plausible option if they knew that they weren't involved. The only other really plausible option is that Madeleine left of her own accord. And since they knew her better than anyone, they would know whether this seemed a reasonable prospect or not. Aside from the question of "why" she would leave the apartment, is the other question of how she would have managed to raise the heavy shutters and then open the window without leaving any fingerprints. Unlike an intruder who would almost certainly be wearing gloves, she would not. So no, if they are telling the truth about finding the window open, I see nothing unusual about them asserting so vehemently that Madeleine must have been taken.
I have no issue with Amaral questioning their account though. In fairness, it would be remiss of him to not consider the parents involvement. Unfortunately, in the case of missing children, it is most often someone known to the child who is responsible. But he went well beyond just "pointing out" there were no obvious signs of an intruder. My issue is with logic of his theory and the reasoning he uses to reach his conclusions. Such as:
"The window wasn't open as Kate claimed because it was closed when the police got there."
Or
"Nobody else could have opened the window because we found no other fingerprints and even though an intruder could have worn gloves, he might not have."
A child could see through this paper thin logic and he is supposed to be a credible detective?
You might think it's a "natural" response to assume there was perhaps no abduction due to lack of traces but do you honestly think the theory he proposes here is any way "natural"?
The implied MMO behind his scenario is just preposterous.