It sounds like you have an arrangement with two blocks (fancy, salty word for pulleys), well, actually three, one on the boom and one on each side of the cockpit? This is how my previous, 21 foot boat was set up, with the main sheet running from one side of the cockpit, up through the block on the boom and back down to the other side, then making a return trip following the same route to get more leverage. I also disliked this setup as the sheet was always strung across the cockpit in annoying ways, but it was livable.
If this is the setup, my concern with simply moving them to the back would be that the angle would change, so the sheet would be pulling more back then down. This would change the pull on the boom, and make it harder to keep the boom down where it should be, it would want to pull up more and mess with your sail shape. It might not be too dramatic, depending on how far you move them, but any change will effect sail shape I would think.
A possible way to fix for this might be to add a boom vang, a line that leads from the forward third of the boom (or so) to the base of the mast which you can use to pull the boom down. I have never had a boom vang on my boats so I do not have much experience there, but I should probably add one to my current boat someday.
As far as moving to a mid-boom sheeting with a traveler (the sliding car on a track) up on the cabin top, I am not sure what that would do, but someone else here will likely chime in on that idea. (Hmmm, they did while I was typing, man this board is fast!) Sounds good to me if you have the room. Be for-warned, travelers are typically expensive I think. You might be able to find a used one, or rig up something if you are creative.
If you have any pictures, that would likely help a lot.
1964 Islander 32
Saint Helens, OR