There are several options, I have done something similiar for a client in the past.
1. Remove unmapped in the advanced tab of the import configuration. However, here you will have to be careful when importing, as things will get implicitly deleted. Personally I don't like this approach.
2. STEPXML import with delete tags. more info you can find online in the help section. However, to get from excel to stepxml is not easy.
3. Use delete flags and a business action embedded in the import configuration. There is quite some setup involved but the result is a transparent and controlled process which is good.
Create a new attribute 'Delete Flag' that is valid for the reference type and has validation base LOV for example. Make the LOV values 'Delete' and that's it.
Now you have the ability to declare per import the references as marked for deletion by setting the value on the flag to Delete. You can pass this from excel by mapping a column and transforming the value, as you wish.
Create a Business rule that looks for the value on the flag and deletes the reference if it has the right flag set.
Save this as an import configuration and embed it in a widget or an IIEP.
If you have questions , don't hesitate to contact me.
Regards, Edo