A pretty good answer would be that...a theory is debunked when it is evident that its proponent is less concerned with pursuit of the truth, and more concerned with a "Special Pleading" style support of his pet theory. It is similarly debunked (or "falsified," though I REALLY dislike that particular definition of the word) when the evidence just doesn't support the given conclusion (upon which the theory or hypothesis is based) and/or it is clear that there are many problems with the evidence....and, in this case, the "problems" are legion!!!
You might also like to remember that there were letters from Mr. Hoover and Katzenbach urging that the American public be immediately "sold" on the idea of a lone, crazed assassin, which strongly smacks of a hidden (perhaps duplicitous) agenda of the feds.