That sounds expensive to me I just paid CMW m/c's £402.00 including VAT. I would shop around a bit more the quoted price from ducati dealers can vary by as much as £200. I was quoted £650 for the same service by my local dealer. It could even pay you to travel to a recognised ducati specialist. JHP or Baines may not be cheaper but you know that your getting a top class service.
I think you'll find that ducati accept that the likes of sigma and JHP are as if not more qualified to work on ducati engines. That said it may be worth the price of a phone call to ducati uk to check that the warranty is not invalidated.
Ducati Manchesters service prices are ... here. Are you talking about the 6000 mile/ 2 year service at those kind of prices? My 996 (at 2 years) cost £487 including belts and clutch plates with DSC discount at Duc Mcr in March this year. The 12 month one was about £150 at the supplying dealers.