I'm pretty sure everything needs to be in the same booking to use the GGL redemption. So you wouldn't be able to book her differently.
Throwing her return away (ie just three of you show up at check-in on the return) won't be a problem, just a waste of avios ;-)
You may find that it is possible to call up AFTER you've done the outbound journey to split her off the main PNR, and change her return flight (although you might need to accept a downgrade for her for availability reasons or because she's not travelling with you any more depending on what sort of upgrade vouchers you've used - if possible use a GUF1 for her rather than a GUF2...).