No, we don't go with "the evidence we got". That's not the way it works in this country.
The state is supposed to do a proper investigation and prove their case beyond a reasonable doubt. There are threads all across WebSleuths of stalled cases where everyone knows exactly who the murderer is, but there isn't yet sufficient evidence for a conviction.
Why was the commonwealth in such an all-fired hurry to prosecute this one? They can't even settle on a timeline because their investigation was so poorly done. The facts are not inscrutable. If they had properly documented and photographed everything, recorded their interviews, searched the home, and so on, there would be no question who John's killer was. They didn't so that, so that's why we are where we are.