Having NGOs conduct killing on behalf of the government is a tried-and-true method of counterinsurgence (South American paramilitary death squads for example). The plausible deniability introduced by working through a proxy allows the government to conduct more politically risky operations (including false flag attacks if public support is waning). Criticizing the government becomes riskier. And, if not held in check, the paramilitary elements will inevitably use their power for their own objectives.