I really want her to have taken him and not hurt him/killed him because 1) I don't want to think of him as dead and 2) I want it to be her and not a child predator because there might be a (smaller) chance that she wouldn't have killed him, as opposed to say, a child predator who more than likely would have. Maybe she took him someplace and locked him in with some food and water (okay, I know I'm dreaming) and had planned to kill him later. But, never got back there because LE figured it out too quickly. Maybe LE is just waiting for her to crack and the letter from Kyron's mom was another tactic to try to make SM imagine her own little girl in Kyron's place.
Another scenario that I can think of is that they do have another suspect who they believe abducted Kyron from the school (someone Kyron would have trusted enough to allow himself to be taken by this person) and the SM knows who that person is but is protecting that person (father? SM's older son?)and they are trying a tactic of making it look like they are going to charge her with the crime, so that they hope she, or this other person, will crack and come clean.
I know this is something that would only potentially happen in a made for TV movie but I really want to believe that Kyron is alive. In my version of this story, at the end, no matter who did it, Kyron is found alive and safe. And the person who did this is put away for the rest of his/her life so they can never harm anyone else.