Something along the lines of mass jailings instead of mass killings. And less use of paramilitary forces to execute suspected communists and more use of legitimate military units to find, capture, and try suspects in courts or at least military tribunals.
That's a respectable position, and certainly the preferred option. My only critique is that there will inevitably be situations where simply shooting the bastards is necessary. For example, Allende's bodyguards and loyalist officials of his regime were for all practical purposes legitimate targets during the coup. Several of them put up resistence themselves, and others had the potential to make the Allende resistence much stronger than it was (and thus more difficult to suppress).
In other cases the assassination of Allendist remnants is actually fairly analagous to somebody like Muqtada al Sadr in Iraq today, or Uday and Qusay a couple years ago. If some nutcase, be he communist or islamist, is hiding in the countryside or in neighboring countries, and trying to round up guerilla fighters to attack the existing government for not being communist/islamist enough, then shooting him or bombing his car often the best policy. Pinochet did just that.
You're right that he also harmed innocents, and I don't think anybody would deny so. What should be noted though, is that as far as similar scenarios of overthrowing communists, islamists, nazis, marxists, and other murderous thugs of that sort go, Pinochet's coup was a very very very mild comparison.
More innocent civilians died from brutalities committed by troops on both sides in any given year of the U.S. Civil War than in the entire two decades of Pinochet's regime. Yet I don't see you calling Abe Lincoln a murderous thug.