If Trump gave them blanket clearance, it would then be legal. Don’t think it would be wise or prudent, but...until he does, any Cabinet Head visiting a SCIF needs to submit their paperwork showing they have access. Or they can have temporary access but the SCIF will first lock up some things.
I’m not saying all compartmentalized info needs to be compartmentalized. But the people running the SCIF do not control that. They do have legal responsibilities and could/would go to jail if they do not follow the law.
I think it would be ok for anyone who felt legally obligated to keep a cabinet head out of a SCIF to ask the cabinet member to sign a written “release”—could just be a paragraph—saying the cabinet member was over-riding any previous legal instructions and took full responsibility.
That would protect the employee in case of later legal action.
This seems to me to a bit like a military sentry guarding a secured location, ordered to allow no one pass, but those on the list, refusing entry to a senior officer. If General "X" isn't on the list, the sentry is supposed to keep them out, whatever his or her rank. The General can order whoever makes the list put the General on it, and then enter, but can't order the sentry to admit them without being on the list.