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Just after posting on here I actually sent John Lewis an email with the exact points you said. I included a link to the apple charger on their own website were people have left negative reviews due to having the same cable fraying issue.
farewell-
John Lewis sucks sometimes, tell me it's not their Oxford St store? I wanted to returned a brand new tablet a while back, only opened it to test and didn't want it, so returned it the next day or day after, they refused to take it back as it's been used, I had to kick up a fuss and refused to leave until their department head came out from hiding to speak to me and take tbe damn thing back. They said once an item has been opened, even though it is still in its original package, it can't be returned. Bullshit.
ExTra
I would send a letter of complaint to John Lewis saying you were not impressed with being accused of intentionally damaging the faulty product they sold you and highlight how common this exact issue is by pointing them at any number of these images online...
https://www.google.co.uk/search?q=macbook+charger+worn+out&safe=off&espv=2&biw=1436&bih=780&source=lnms&tbm=isch&sa=X&ved=0ahUKEwion6KOhN3PAhXO0RoKHRZ6BLoQ_AUIBygC&dpr=2