Hey Dirk,
This is from the Chicago Manual of Style (used by many agents and publishers), section 8.22 civil titles: "Much of the usage below is contradicted by the official literature typically generated by political offices, where capitalization of a title in any position is the norm (see 8.20). In formal prose, however, civil titles are capitalized only when used as part of the name (except as noted)." Here's the specific one you want:
"the secretary of state; John Kerry, secretary of state; Secretary of State Kerry or Secretary Kerry". This seems to indicate you should use secretary.
Hope this helps, Regards, Randall