Okay, so I know that I can't kill them until I've done some research, and that's fine. But I can't even seem to stop them from wandering around by base, blowing stuff up and killing the minions. I had some success with one of them by doing the mental attack until she'd lost interest and wandered away, but every time one of my minions gets close to Jet Chan, he kicks them in the head and they die - before the minions can do anything to him at all. Is there any way to get him (and the other super agents) off the island?

Usually I tag them for capture, then immediately interrogate them.
After the interrogation is over (if they didn't escape it) a minion will carry them outside and when they wake up, they leave.

I used valets to drain their attention, then they become zombie like and a valet leads them waaay outside.

Heh, bastards are tough. Spamming them with valets and the like is nice, but problems arise when more than one agent spawns at a time. Once I had four of them spawn, i just reloaded an earlier save, lol. Also, even after zombification, valets often just lead them outside the door, then they recover in a while and begin anew. It is also very hard to interrogate them, they usually escape the very moment they are locked in a cell.
Other problem is that they basically lock down my base, even if i manage them. If i happen to assign a mission, they like to slaughter all those mercenaries, spindoctors etc. running to da choppa. So I learned not to assign missions when the trigger happy fellows.
The ladies and Rambo are reasonably easy to charm, that is, if a valet manages to reach Rambo through his field of fire. At least Rambo has low smarts, heh heh.
Bruce Lee is damn annoying - he is fast, loves to one-shot my henchmen and kills everything. Still, it is James Bond who is the worst, with his extreme stats.

I had some good results by attacking them with my henchman, and then leave them barely alive. They will respond the same way as regular units and leave.

I had an army of diplomats, spin doctors and playboys (10, 5, 10) and they all hang out near the entrance.
i just tag superagent and they weakened him... he managed to kill one or two of my minions but rest of the bunch managed to get him.
and when a superagent was being weakened i order all my henchmen to beat the crap out of him. when 'dead' they stay down for quite some time.
if a superagent was too dangerous and none of my minions could come even close to weaken him i used jimbei to attack him allowing superagent to concentrate fire on him instead of social minions who could approach him without getting killed.
then jimbei would use windwalk to escape the death. but social minions would be able to do their job then.
Finally i would send my other henchmen to finish the job beating the crap out of the agent.
One should never allow three or more agents to be present at a single time on the island. the heat level is the biggest reason why they are there.
no missions on more than two areas at a time. and cooling off periods are helpful when there is a single mission or none at all happening.

How I dealt with the agents basically depended on what agent it was, with the agents falling into two general classes. Mariana Mamba, Jet Chan, and Katerina Frostanova are what I'd consider low threat agents. They can simply be tagged for weakening and social minions will prevent them from causing any serious trouble. The occasional minion will still get killed (or desert) but most of their time on the island will be spent essentially comatose from having their stats drained. In stark contrast, Dirk Masters and John Steele are what I'd consider high threat agents, and will cause absolute havoc if you just try to weaken them (as they will just start mowing down all minions they see at a distance). My way of dealing with them is to tag them for capture, then bum rush them with several henchmen (usually will set Kane and Eli on them, then have Jubei teleport right next to the agent so Kane and Eli can close the last bit of ground without being fired on). After capture I'll then interrogate them with an attention draining device (such as the AI computer), after which they'll be escorted outside the base and will usually then just head home (draining smarts seems to result in them going back to shooting minions much more often than draining attention does).

i always put mamba in the mixer tough. she makes nice sounds when in there and it looks so dirty :D :D :D

Spoken like a bunny =3 I approve

Same as what I do with most other pesky intruders: tag them for capture, interrogate over and over until they lose all heat (and then some - want to ensure their time on the island is up). Then let the valets escort them out and wish them a nice trip home.

The difference is they're both harder to capture and harder to contain.

For the first, setting up the base so that your traps do most of the work for you is the best. In this case, don't tag them until they've already passed the heavily trapped areas of the base, or they end up unconscious, whichever happens first (if traps in base are well designed, the latter should occur more often).

If they've already passed the traps, then tag them, again if the base is well-designed hopefully you'll have tons of minions on their ass. However, with super agents it's not worth taking chances, so I usually then grab a henchman, get him to grab a bunch of minions with them, and use them to capture the agent. The only thing to watch out for is that henchmen taken down by super agents lose one of their lives, and if they lose all of them they're permanently dead.

For the second, it's worth having an "extra secure" security section specifically for super agents. You want a cell, surrounded by so many traps that they're knocked out as soon as they step one foot outside their cell. Knockout bees are great for this.

Alternatively, or additionally, you want an overstaffed security room connected to a nearby barracks/break room (and not too far from the nearest mess hall). I put this stuff deep in my base, usually with a separate security circuit just for this. That way, any escaping super agents are immediately swamped by minions, since they keep their tag when they escape. Just make sure you have cameras everywhere.

haha

Took few minutes for me to remember wth i was talking about. have not played the game since then.