Hi,
Yes, by default freeze acts on the complete system. If you want to freeze orbitals belonging to indivual atoms, you might need quite a bit of handwork (depending on the system). Is there some reason why you don't want to freeze all core orbitals? And if you are not freezing all core orbitals, are you sure that your basis set is able to describe the correlation within the core orbitals? DZ sounds a bit smallish to me.
Antti