What options are available? I am considering taking off the wheels if there is no other good option, and putting it inside some kind of luggage bag.

One option is to get a cardboard bike box from your local bike shop; they must throw dozens away every week.  

 

You would need to wrap the bike well - pipe insulation may protect the tubes from minor dents.  

Also try to get a spacer or old axle for the forks, to reduce the risk of them getting bent under the weight of bags piled on top.

 

I'm in the same position for my next trip to Langkawi, as I don't want to drive and ferry again, but a proper travelling bag or flight case would cost thousands of baht.

 

A friend suggested just using the plastic wrapping machine at the airport on the naked bike (after removing handlebars, pedals, derailleur, but I doubt it would survive unscathed

 

SC