I think it was evident to me, and this belief was validated in the Star Trek: Ongoing Issue #21, that Admiral Marcus considered the Enterprise
Captain Robert April:
I'm sorry, Kirk, but your Enterprise was expendable given the fleet that Marcus was building.
According to the movie, Admiral Marcus approved the mission of the Enterprise
. She would carry 72 advanced torpedoes, with the intent to kill Khan on the planet Qo'nos. As the ship approached Klingon space, the starship's warp drive malfunctioned - a malfunction initiated by sabotage committed by Section 31. If the Enterprise
had completed her mission, and had fired the missiles, the Klingons would quickly locate the origin of these missiles and destroy a disabled starship, a preamble to war between the two galactic powers.
Admiral Marcus' decision to destroy the Enterprise
was his attempt to ensure there were no witnesses to his actions.