I have not been there so have no first hand knowledge.
However, in checking their brochure on line, it appears that, in most cases, the trips on the WSF are round trip, WITH THE EXCEPTION of this particular trip.
Fares
Passenger fares are round trip, with the exception of the Port Townsend/Coupeville route and sailings to/from Sidney, B.C. Please refer to the Passenger and Vehicle Fares brochure (pdf 228 kb) or call our information staff. You can pre-purchase your ferry ticket.
I'm reading that to mean that each leg in either direction, you have to pay separately. So, you pay departing from Coupeville, and you pay departing from Port Townsend. At least that's how I'm reading it.
Hopefully, one of the locals can confirm or correct my reading of this. This would be interesting/good to know, since I've got a long range trip planned for this area.