Even in the absence of a governmental agency, there is another method to control these covert operations, and that is public opinion. As the news of many government atrocities has become known, there has been a great public outcry against these occurrences, and at least some times, this has led to modification of policies and covert actions. For example, when the atrocities at Abu Ghraib prison became known, there was a moral outcry to stop the offensive practices and punish those who had participated in them. Obviously, covert actions are not going to become known overnight. However, as they do, the citizens can make their feelings known and cry out against these types of outrages, encouraging leaders to stop using these covert actions in the future.

Finally, we must enact legislation to ensure these types of covert operations do not occur. While anyone can find loopholes in legislation, without it, there can be no effective oversight or control of covert operations gone bad. The U.S. already has a policy against assassination, but...

Thus, legislation is not the only answer, but it does send a strong message to those in power. If the American people want actions like this to stop, they have to enact legislation, create an overseeing agency, and make their feelings known to those in power. That is one way to ensure that incidents like this do not continue to occur, especially with the blessing of those in power or with personal agendas.
References

Kibbe, Jennifer D. "A Loophole for Covert Operations." Brook.edu. 8 Aug. 2004. 23 Feb. 2007. http://www.brook.edu/views/op-ed/fellows/kibbe20040808.htm

Wachtel, Howard A. "Targeting Osama Bin Laden: Examining the Legality of Assassination as a Tool of U.S. Foreign Policy." Duke Law Journal 55, no. 3 (2005): 677+.

Howard A. Wachtel, "Targeting Osama Bin Laden: Examining the Legality of Assassination as a Tool of U.S. Foreign Policy," Duke Law Journal 55, no. 3 (2005).