You should have no trouble getting back on the ferry after the encounter. I believe there is a ferry at 2pm and 4:00 or 4:30pm. You will have to catch the later ferry. I would suggest you go over to the island earlier than your 2pm appointment and spend some time on the beach.
If you book through Disney, they walk you to the ferry and tell you how to get back. They also serve a lunch on the island. (not sure if it is any good, didn't eat).
I really wanted to book through Disney because we needed the earlier appointments with the children. IF you don't care what time your Dolphin Encounter is scheduled, then scheduling yourself will save you quite a few dollars. Disney has the monopoly on the 9:15 and 12:30 appointments...that is why your appointment is booked later in the day.
It is about a 1/2 mile walk to the ferry, probably less. My 4 1/2 year old had no trouble walking there but was a little tired walking back. He made it though!
Once you get off the ferry, you walk a little ways down the beach to the encounter...maybe 1/4 mile, probably less.
Hope that helps.