And even if he was that clever at manipulating people, how was Hannibal really able to do it without getting physical with Miggs or giving him drugs etc?
And what, based on a few words, Miggs would just develop a conscience like that and agree to it?
Plus, for all his wrongness and unlikability, why was Lecter so keen on having Miggs be dead, even if he did do the terrible thing by throwing his semen item at Starling and perhaps guilty of some or other type of criminal offenses, why did he even want him to die?
That's not a problem. Lecter is supposed to be a unique kind of psychopath. He is a narcissistic genius and whatever whim he happens have... he will take action to make it happen. Lecter has a weird obsession with "politeness" and a highly personal attitude towards the mere humans around him. Thus, having a strange fondness for Starling, he reacted in an extreme way (extreme to us) to Miggs for having behaved in such a grotesquely impolite way to her.
It's like how in Red Dragon we learn that a minor imperfection in the playing of a symphony musician led Lecter to kill the man and feed him to some folks he did not respect...