That weekend, well, any summer weekend, can be tougher than weekdays in getting to/from the SJIs. You should arrive at Anacortes at least two hours ahead of scheduled departure. Read the Inside Page, below, about your return to Anacortes.
This Inside Page might help you make decisions, not only about the ferry but also whether you want to go on a charter or try to see the whales from Lime Kiln Point State Park or the southern end of the island, off Cattle Point and South Beach.
If you see whales on a charter, great. If not, the "guarantee" might be good only if you see no mammals at all (unlikely) and it's for a return trip, not a refund.
There is plenty to do (on San Juan, my choice) for you all. If you wish to see Orcas Island, definitely take the car and drive up Mt. Constitution.
San Juan Islands (Information on the several major islands, with key websites.)
Whale Watching Information
On the other hand, the kids might like playing on the beach at Ocean Shores (or any coastal area).
In any case, you want to do your lodging searches as early as possible.