2 night on the Olympic peninsula is adequate so given your time you should have plenty. Take a ferry over to Whidbey and an overnight there should be enough. As for getting back to SEA, it should be an hour drive time from Mukilteo (just be aware of ferry waits if any) or about 1 3/4 hrs from the north end by I-5 (even detouring around the Burlington bridge out).

As far as getting back from the Olympic peninsula to SEA, it will take a little bit longer. Wouldn't stay anywhere except at the south end depending on your time of departure.