Have you had a look at the scratches, because they may be on the inside where he's tried cleaning it himself? I wouldn't just cave in and accept responsibility because I feel you would have noticed if you had inadvertently damaged the glass in question.
Did you check the conservatory roof guttering for pieces of broken roof tile which may have caused the damage to the glass.
I had to sit down with my insurers and verify everything I was covered for and the long and short of it was that if my job specification stated that I cleaned conservatories internally and externally then I was covered for accidental damage.
You sound to me that you don't feel that you caused the damage and you should go with that gut feeling in defending yourself and sticking to your guns. your insurance company wont just pay out if you don't think you damaged the glass it may be up to the customer to pay for an independent damage report to be carried out, which will cost him if its not proven.
Two thought spring to mind - did you take any pictures of the conservatory roof before cleaning because if you look carefully you may be able to see damage before you started also if the conservatory wasn't that dirty in the first place then you may have been set up for this.
If you want me to examine the pictures using photo shop I am willing to do this for you.