Have you ever seen a Moore film? He's not a lunatic trying to connect red strings, he's a filmmaker who edits and manipulates his movies to gain emotional responses to the events on camera and a pro-working class angle.
You literally opened this thread asking how bad it will be and characterized Moore as a cartoon character.
The movie will likely do what Moore does; capture the spirit of the story. It won't be factual, and it will be somewhat convoluted, but if Moore is good at one thing, it's that he can create a narrative that captures the spirit of the story, and if a conspiracy is presented, it won't be a tin foil hat lunatic, it'll be a (bias depending on Moore's personal beliefs) articulate and coherent presentation tied heavily to the emotional shock of the assassination. We'll possibly see some Northwoods stuff tied to a Business Plot, but unlike Oliver Stone, Moore is smart enough to not straight up disprove himself in his own film.
You have a point, it might well not be as convoluted as all that.