Ironically, we, too, will be on San Juan Island that day and 4 subsequent days. :)
We enjoy hiking and birding, so keep pretty busy regardless of the weather.
But for visitors, here's my take - the daylight hours are relatively few; the water is cold so any wind off water will be very cold; if it rains, vertically or sideways, you'll probably be indoors and will not experience the islands.
On the other hand, the weather could be like today, Sunday, on Whidbey Island, and it was glorious. And could be there, as well.
An overnight would be nice to explore at least SJI; more time, would allow a look at Orcas Island, but less to do. See article, below.
I'd play it by ear, tracking the weather reports.
My recommendation would be, rather than the San Juans, spend a day, perhaps an overnight, on Whidbey Island. If the weather is good, it's beautiful with lots to see and to do, from the small artsy towns to Deception Pass (even a ferry to Port Townsend and back).
If the weather is not so good, you can still do many things, but return to Seattle as you wish.
Whidbey Island (Great day or more getaway that is iconic of the Pacific NW, with key websites.)
Ebey’s Landing State Park, on Whidbey Island – Dramatic, easy, trail, farmland to the east, Puget Sound and the Olympics to the west.
For ideas on the islands...
San Juan Islands (Information on the several major islands, with key websites.)