Amaral takes one of the possibilities from the files as his thesis and attempts to prove that it is the correct thesis. The judge didn't rule on the correctness or otherwise of his conclusion, she just said it upset the McCanns. The presumption of innocence was ruled upon, so it's very important. I don't know if an ex policeman has to uphold the presumption of innocence of everyone or just of suspects.
I can see your question... but it's not just that he's any old ex-cop, he was the coordinator and therefore could be assumed to know what he was talking about.
There must be all kinds of permutations... What would be the situation if he accused Mr Joe Blow? If Mr Blow had made an innocuous statement, but which appeared to Amaral as highly suspicious due to gut feeling... should those suspicions be made public? What if Mr Blow had never even been officially interviewed? Does that change anything?
Loads of people can become "persons of interest" at some point during a major investigation... It doesn't mean that they dunnit, though, does it? Nor that their names should be dragged through the mud as if they had done. And in particularly emotive cases such as the disappearance of a child, or even the suspected rape / murder of an adult... you and / or members of your family can be exposed to misguided vigilante action.
How on earth is that considered "normal" in a civilised society?