Did you remember to hide all your team members as well? I think the code checks to see if any of them are visible as well once you try to do a "silent kill". And to be absolutely sure, try it when there are no civilians around, if they see you and are allied with Pedro's faction everything will go pear-shape.
And this mission is very tricky, it can take up to 20 tries before you actually succeed, so be patient.
Good luck
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