I know this is a bit late, but if there are any others looking to do this, you *can* leave your bike at the port in La Cieba. However if you are intending to be on the islands for more than 10 days, it is cheaper and *much* safer to take it with you. Alternatively, Heidi at hotel Rotterdam in La Cieba (She runs the cafe next door) regularly puts bikes in her garage for people.
.. and if you're passing, I'm on an extended hiatus from my trip, and am currently working on Utila. There's another guy like me here who is a good bike mechanic and knows the KLR backwards. (he's just rebuit a shock for another biker who came past)
Stop by and say hello. I can be contacted by emailing though the site, or stop into Altons. I seem to be there all the time at the moment!