Yes, hotel rates in the Accommodation Page are not cheap. but the contracted prices are the best we could find with the travel agency, and as long as I saw on the internet, they are cheaper than original prices.
Another option, recommended because of the price, is HOTEL CO-OP IN KYOTO http://www.coopinn.jp/ but we where unable to contract as a group. Maybe you can find room as individual. It is situated in the center of the Kyoto city, but 25 minutes walking (2.2 km) from the Congress Venue. You can take the subway, it is one station but here you also need to walk a bit too. 8 minutes by taxi.
Another is Harton Hotel which is included in the accommodation site. This is usually cheap but as Kyoto is now under a so called tourism boom, hotels rate are very high, also for us people living in Japan.
The cheapest option are the called here “Guest House”. Usually they are shared rooms, used by backpackers. I make a Google search for guest houses in Kyoto. Here is the link: http://j.mp/guest-house-google-map
Also you can take a look at Air B&B (https://www.airbnb.com) It is possible that you find room at very nice rate.
These are some recommendations I can give you related to Accommodations in Kyoto, hope this information would help you. Note that I can not help you to make reservations in other places than the proposed in the Accommodation Page. Thank you for your understanding.