The shuttle bus runs to a timetable which it adheres to pretty tightly, so with a bit of planning you should be ok. If you do miss it, then from memory it is a short walk (5 minutes) down the road to a bus stop with services through to town.
We certainly came back to the hotel this way when travelling on a bus card when were in Kyoto, but we always caught the shuttle bus in to town and Kyoto station.
Hopefully someone with a slightly less hazy memory of the bus service will be along shortly to confirm or correct me!