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Is she fixed or SS? Could convert to flats and SS if she's getting wary of fixed and the toe-overlap, though I realise that's not actually a solution for fixed toe-overlap. I know 'get used to it' is not very helpful (although it is true and I started out very worried about - I'm 5'7 so all my bikes have had noticeable toe-overlap - but over time it's faded into the background issue-wise). Another option is to take off the front mudguard? I know front mudguards are nice to have but some soggy toes might be worth it for more confidence on the road, especially in the dark winter.
TL;DR
If she's fixed, take off the mudguard.
If she's happy to swap to free, ditch the cages and swap to flats and SS cog.
If she's free, ditch the cages.
She's having problems with it, and it's making her less confident in traffic too. I'm not sure how else to correct it without taking the cages off again.