Same happened to me about 6 months ago!
Had mine repaired at VW, bonnet wasn't damaged but had that Resprayed as well as blending in the wings and think total cost was £1,500, although I put through insurance so just paid the excess and for the bonnet which was about £500.
I just took it as a positive as got rid of all the stone chips and a nice front end re-spray....although the deer didn't see it that way!