To kill Nunez silently, first make sure all your mercs are out of sight from the natives, if they are seen by the natives when the shot is fired they turn hostile. Make sure you do it at night when it is dark, I usually succeed between 2-3 am. Use the silenced USP provided by Nunez and shoot him in the head a few yards away.
It might take a few re-loads, but it works eventually if you find the right spot to shoot from. Oh, and make sure there are no civvies around, I usually point my gun at them and they run away out of sight.
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