Super Agents are the source of anger issues for anyone who has played this game. Here are several ways in dealing with Super Agents:
1. Social Minions. The weaken tag does slow down their progress. However the downside of using social minions is (a) They killed after performing the task (b) The stats of the social minion fall drastically, thus unable to carryout normal tasks until full and (c) it takes forever for the Super Agent to lower its stats.
2. Sentry Guns. ARE the MOST EFFECTIVE WAY in dealing with Super Agents. Though you need a dang lot of them in a very good location. Place sentry guns (e.g. presumably near your base entrance) in such a way that they can attack and also protect themselves. Also, using the "Capture Tag" on super agents is more effective than the "Kill Tag" in bringing them down. Be sure to have Fire Extinguishers nearby.
3. Weaken Tag Bug. If Super Agents somehow get through your defensive Sentry Gun line (which means they're already in your base), don't rely on traps as they don't do squat to stop Super Agents. There is an odd bug that is quite an equalizer in handling Super Agents: Use a weaken tag on the Super Agent, after a social minion will start to perform his task, quickly change it to kill or capture tag. You will notice that the Super Agent will continue "acting" as if still under the influence of the social minion, all though the social minion is no longer performing the task. Repeat this process before the social minion get too far. You will notice as you do this, construction and military minions will attack the super agent when you issue the kill/capture tag, but will continue to attack even after you've re-issued the Weaken Tag. Experiment with this method and you'll discover that sometimes the Super Agent just stands still while your minions punch away!