Well she was obviously making an excuse to be there and everyone in the room knew it. Id guess the security clearance was something like manually verifying his identity and registering him with the computer as part of the command staff. This would normally be the sort of boring paperwork the computer or a lower level security person does off screen, but she wanted an excuse to be there and the clearance was technically something she was responsible for.
When she and the alternate Kirk went on their little time travel adventure, the episode ended with La'an calling Kirk to ask about some kind of bullshit info she needed for Sam Kirk's file.
I saw the whole security excuse as an extension of that.
Kirk is temporarily transferring to the Enterprise, so maybe she needs to get him set up with XO-level security credentials in the computer. (The kind of thing you need to do, “Computer, eject the warp core, authorization Kirk lambda two six two.”)
That suggestion actually makes sense: a standard procedure that doesn't apply for the vast majority of officers beaming over.
The phrasing maybe a little awkward, but it works. Nice one!
I think we all know what "security clearance" she wanted Kirk to "run through..."
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