I have an Accord also, manual transmission included, and I have always put my bike in the trunk with the back seat down and front wheel off. I also remove the saddle as it allows me to push it in easier, but it can fit with it on. I have even placed my gf's bike on top of mine in the back seat with the front wheel off.
There is 200k miles my Accord, so I have some time left, but my choice of replacement vehicle would be an Impreza hatchback.