Allow me to chime in here, as I have to worry about WA smog with future Megasquirt...supposedly you can wire up MS in parallel with the stock ECU such that everything is still ECU controlled except fuel/spark. Almost like using it as a piggyback. This may involve duplicate sensor wiring for whatever sensors MS needs (O2, RPM, etc), but otherwise should leave OBD2 diags compliant.
www.sparkandfuel.com used to have a section detailing a little more about this, but it's buried and I don't have a lot of time to dig for it.