The user-friendly way of separating ROMs from emulators is simple.

1) ship emulator without ROMs (or any other copyrighted material you don't have permission to redistribute!)
2) When emulator starts and it can't find the ROM it needs:
- show a popup "download ROM files [ok/cancel]"
3) hitting OK the emulator proceed to wget the rom file from a host online.

This ofcourse means the emulator developer needs to find a web host for the roms, which will then take the legal risk. Indeed, the people in this thread who think roms should stay, would probably make the best candidates as hosters