Khan transported himself to Kronos so that the Federation couldn't reach him. If any Starfleet ships entered Klingon space, that would be a sure way to start an all out war.
The purpose of the special torpedoes would be so that Kirk could kill Khan without entering Klingon space. The original plan was to fire them from the Klingon border and kill Khan without being detected. (Of course, since Marcus's goal was to start a war with the Klingons, I'm not sure if the attack would actually go undetected.)
So the special torpedoes were needed so that Kirk could attack Khan without entering Klingon space. I can't remember if the number of torpedoes was mentioned in the conversation between Marcus and Kirk, but even if it was (which would indeed appear to be overkill), at that point Kirk was blinded by the desire to get revenge for Admiral Pike's death. Since Marcus was willing to re-instate Kirk as captain of the Enterprise and give him the opportunity to get revenge, he would probably go along with almost any plan Marcus could come up with.