Who is marrying her suggests an action on the side of the groom. In Czech it would be "Kdo si ji bere?" Koho si bere ona? suggests an action on the side of the bride. The word 'brát" also means "to take" in Czech. If we temporarily put that word in (though it is not used for this situaton), it will make things little clearer.
Who is she taking? = Koho si bere ona
Who is taking her? ´Kdo si bere ji.