The way to deal with MS 13,"Zeta" commandoes and other criminal gangs is to end the War on Drugs. Pull the financial rug out from underneath them. The War on Terror cannot be won as long as the WOD is being waged. Drug prohibition funds our enemies both foreign and domestic. The financial and human resources squandered on the WOD could be better used to protect our borders and prosecute the War on Terror.
Sombra Negra seems to have found a fairly effective way to deal with ms-13
From wikipedia:
Sombra Negra hunts down and executes all types of criminals, but it is well known for its specialty in pursuing and executing members of the notorious El Salvador-based street gang Mara Salvatrucha (MS-13 or MS). The MS-13 gang is considered the most dangerous street gang in the United States by sectors of the U.S. law enforcement community. Nevertheless, Sombra Negra is rumored to match the MS-13 and possibly even surpass them in terms of violence and brutality. Sombra Negra has already claimed responsibility for the deaths of several MS-13 members in El Salvador. It is reported that members of MS-13 are so intimidated by the Sombra Negra that there have been several documented incidents where MS-13 members have attempted to hide their membership in the MS-13 by pouring acid on their MS-13 tattoos (which identifies them as MS-13 members) and then using a cheese grater to scrape off the skin. Many members of MS-13 reside in the United States illegally and are afraid of being deported back to El Salvador because they fear they will face certain punishment and/or execution at the hands of Sombra Negra upon their return.