Ki-Empowered Strikes aren't magical attacks to begin with!
Ki-Empowered Strikes state this explicitly:
your unarmed strikes count as magical for the purpose of overcoming resistance and immunity to nonmagical attacks and damage
This ability makes the monk's unarmed attacks count as magical only for the explicit purpose of overcoming resistance or immunity to nonmagical attacks and damage. They're not magical attacks as defined by the Monster Manual ("a magical attack is an attack delivered by a spell, a magic item, or another magical source"), and they don't count as magical for any other purpose, such as when considering resistance or immunity to magical attacks and damage, like your monster has. The damage the monk does with their unarmed strike is still mundane bludgeoning damage at the end of the day, it just has this special property that allows it to hurt creatures that would normally be resistant or immune to such things.
Though your monster is immune to damage from magic weapons, that affords it no protection against the blows of a 6th-level monk. In fact, as your monster is both resistant to attacks from nonmagical weapons and separately immune to attacks from magical weapons, as written your player's monk would be able to deal it full damage despite its combination of resistances and immunities, as her strikes will overcome the nonmagical resistance yet do not interact with the magical immunity.
For balance purposes, you may wish to rule (and I probably would rule) that the actual result is that the creature ends up with resistance to the monk's attacks, as if the monk gets to choose the most favourable option between her attacks being considered magical or not; or you could rewrite the monster to be resistant to all physical damage and additionally immune to physical damage from magic weapons, so as to overlap and prevent the monk accidentally loopholing around them.
