Yes, the MC was caught hiding weapons under her skirt, so he vetoed skirts.
If one joins the the cheerleaders, presumably the uniform will include skirts for females.
However, I doubt CIA daddy would mind too much.
The shorter the skirt the less weaponry one could hide, after all.
So I imagine it’s banning long skirts he really cares about.
Which means that if I’m right, the total ban was from CIA daddy’s discomfort over arguing over skirt length with a traumatised teenage girl, or CIA daddy not having the patience to figure out through trial and error the skirt size that can hide an acceptable to him amount of weaponry.