How deep are the scratches?
Which brush are you using?
How long have you been using WFP on the windows?
It's a very hard thing to do, to scratch glass with a WFP brush but it is possible if you have grit in the bristles. I've stopped using flocked brushes for that reason now. I think I put a light scratch in some glass but you can't notice it unless you stare very hard.
Use a mono filament brush and good flow rate, as long as you keep the bristles on the glass and not the stock of the brush, then you should never scratch Amy glass.
If it is just two pains of glass then it will be cheaper than your £250 excess to get a local joiner out to fit new glass units. Still though I'd be very reluctant to go down that route.