Are you sure you won't want a car on San Juan Island? Will you have bikes so you can explore? We spend a lot of time on Orcas Island (family home there) and wouldn't want to be there without a car or bike, since there are so many great spots to visit on the island, and it is rural and quite spread out.
The advantage of walking on the ferry without a car, though, is huge. Waiting in the ferry lines with a car can take hours during the busy summer season (6+ hours is not unheard of, I once waited 10 hours coming off Orcas back to Anacortes), whereas walking on the ferry you can get on any boat, no wait involved.
Have fun, it's a beautiful part of the world.