The trick to dealing with the super agents (well, any agents, really) is to confuse them, rather than try to kill them.
It's been a while since I played (but now I'm going to have to re-install it), so I don't remember the exact attribute to use. Seems to me that it was the valet looking guys...
They don't actually attack anyone - they just politely direct folks to the beach, or the hotel, or offer them a drink, or whatever. It confuses the agents and makes them forget what they're doing. After a few rounds of this they'll wander back home without actually causing any harm. And there are traps that affect the same attribute.
Plus, being non-lethal, it's not so painful if your own minions trigger them.
I used to fill the entry hall of my lair with those traps, and then recruit a bunch of the appropriate minions. Never had any trouble with the super agents. In fact, it got a little too easy.
And later in the game you can permanently remove the super agents by discovering their weakness and exploiting it.
I did that. Yes, I could get them stunned (trying to kill them is impossible, more on that later), but it took about 10 different spindoctors or so to do it . And believe me, I had that many spindoctors lying around. That wasn't the issue. The issue was that they would just fuck everything up and would never go away. Now I'm cool with them killing a few minions each time they show up or getting a bunch of heat by breaking into my doors or even teleporting into my base or digging down walls or what have you, but what made it suck was that they were just unstoppable. They wouldn't go away and had the annoying habit of killing all of my traps not located at the front door, killing my traps located at my front door while the spindoctors run out, killing my security system so the spindoctors don't run out anymore, and killing a buttload of minions, agents, and tourists from the exploding traps and doors, all of which costs me time, money, or both to repair. So lets just say that each time they get stunned, they take out 1 construction worker, one of each tier 1 minion (valet, guard, and technician), and a single tier two or tier three minion (any of the rest of them, this is being very generous since I usually have a swarm of spindoctors standing around them while a bunch of shit blows out). I believe they stay stunned for about 60 seconds. We'll say it takes 3 stuns to get them to leave the island. We'll say we get 5 minutes between visits to the island. We'll give the super agent two minutes of time to spend wandering around, destroying other stuff, and whatever else they decide to do. That means that every 10 minutes, three construction workers, three valets, three guards, three technicians, and three other minions have died. That's a total of 15 deaths. Now, to meet the rate of dying, I'm going to have to crank up my minion generation a notch. In addition to having to rebuy whatever the super agent destroyed, which by the way could easily be over $10,000, I also have to pay a bunch more for new minions AND spend a bunch of time retraining the minions.
Oh, that's for the ones that DON'T walk around killing your minions. For the ones that do, you're fucked. If one wanders near the depot, you don't collect any cash or get any new minions. If you're sending out or getting a bunch of minions back to or from the world map, they all die. When the Agent does get to the front door, everybody and everything there explodes and dies. Every spindoctor who interacts with the Super Agent dies. Every valet who walks over to put out the fires, every technician who walks over to fix the shit, and every contruction worker walking by with new furniture dies. We'll be generous and say that every round of stunning costs me 20 minions, 18 of which are trained at least one level. I now have to buy minions at a rate of 1 every 20 seconds just to keep pace with the deaths). That's not even getting into the tens of thousands of dollars of equipment that needs to be replaced, the shitload of time that needs to be spent retraining minions, and the occasional "fuck you" that happens when I lose all of the diplomats or commandos and need to redo an act of infamy to get more. Speaking of AoI's, I had so few minions who weren't busy training replacements, getting me money, SCIENCE!ing, or dealing with agents and super agents that I had pretty much none left over for doing AoI. So I did them very sparingly, which is a shame since reading AoI and getting rewards are pretty damn cool. Since I did them so rarely, it literally took RL weeks of playing just to get another 50 fame. My reward for that 50 fame? Like ten more minions and another super agent pissing me off. Motherfucker, I do NOT need another one running around.
Oh yeah, did I mention that three Super Agents show up at the same time? Might be four, I wouldn't know since I sure as hell never got that far (probably not since I had the AoI to get rid of the Asian guy). All of this rebuying of equipment and needing to rebuy minions constantly pretty much drained me of money, which is bad since all of my minions are now dead, leaving me with nobody to go get more cash. Oh, and since three of them are now killing at the same time, I'm either buying minions at 1 every ten seconds or losing minions constantly. Buying them at that rate takes extraordinary amounts of money, so I trained them to guards and shipped them out ASAP. When they died, I'd do it again with their replacement. At the end of it, I didn't even bother training them anymore. I just sent them out as contruction workers. It was too risky to have them walk into my base, train, and then walk back out. It was very risky just to have them walk from one depot to the other.
And the worst part was, it wasn't fun. I couldn't do anything about the super agents. I had three options: kill them, kill them with the help of my henchman, or stun them with spindoctors. Killing them with just minions takes an insane number of minions. Killing them with my henchman plus minions is retarded since that'll make your henchman lose lives. Subduing them is extremely costly, but easily the cheapest method. Problem is, it's STILL too expensive, it STILL leads to a lot of death, and it STILL leads to them blowing up everything! Doesn't matter what you do, what traps you have out, whatever, they STILL blow up everything and kill a bunch of minions. Oh, and my reward for FINALLY getting them off the island? About 5 minutes of peace before they show up again to start the whole process anew. Uuuuugh. And with three of them running around at a time, there was no peace, just moments of slightly less death than usual.
I could of modded them out of the game, yeah, but I didn't. Without them, the game's too easy and simple. Regular agents are a joke to deal with. Anything else that shows up can be easily waited out until your heat goes down OR dealt with by your henchman. So it was a "Damned if I do, damned if I don't" scenario. Rather than play and get pissed of at the super agents constantly or play and be bored constantly, I just quit. Came back a few months later with a mod that let me have a buttload more minions. Didn't help at all since it only delayed the amount of time it took for me to run out of cash and minions. It did, however, buy me enough time to race to the end of the storyline... until I got bored of that and quit, never to play the game again. I'm not even sure if I even beat the story, it was just so frustrating being unable to do anything. Hell, wouldn't shock me if I just simply couldn't get through the story due to lack of minions.
The problem with the super agents was just that they weren't fun because there wasn't anything I could do about them. The rest of the game was fun. Even bands of veterans running around killing everything is fun since they go away eventually They also don't cause my henchman to lose lives, so I'm free to use them. They ALSO don't tend to get too far into the base and are MUCH easier to kill. Bottom line, everything about the super agents was not fun, so they literally ruined the game for me. They still piss me off to this day, and I've not played the game in three years.