It actually is possible to isolate the chunks that have player builds and not regenerate them. This could also be done, as Catty said, via schematics.
The tricky part is that those chunks would not match up with the surrounding chunks, so you could end up with a 16x16 square block floating above a lava pit, or a village underneath a lake of lava. It's probably not viable.
Once the server is all up to date I'll do a test and see what happens, but don't hold your breath.