Just remember that you can always go one step more aggressive if you need to, and always use the least aggressive method as possible to achieve the desired results.
There are different levels of "3M Rubbing Compound", the one you mentioned just happens to be a little too aggressive for the PC. If you haven't done any test polishing yet to see what gets rid of the etching you are referring to, I'd pick a small area, and start with AIO and work your way up the aggressiveness scale from there.
After AIO would be your Optimum polish or 3M PI III MG. If that doesn't work, something like Optimum Compound or 3M PI III RC would definitely do the trick.
After you get the etching out, and you are happy with the car's overall finish (defect free), just work your way back down the scale.
Hope this helps.