Why even let Morpheus and his buddies into the Matrix at all? That technology has existed since the late 80s, so there is no reason at all to not include it in a presumably global network of people you are trying to control. Firewalls can be selective with what they let through or not, so just block off everything that doesn’t come from a robot. Or better still, make sure the machines use one network and just don’t set up any wireless hotspots for the Matrix. There is a reason why hacking wasn’t a problem in 1982, despite what War Games might have suggested; if the computer has no connection to the internet, it can’t be accessed by it. There is no reason why the robots wandering the earth could not use one network that was completely separate from the matrix entirely. That would have left Lawrence Fishburne and Jada Pinkett sitting around looking stupidly at one another, not doing Kung-Fu.
So let’s just assume that the human resistance is super clever and they have found a way to hack into a network with a firewall; who knows, maybe they inserted virus software at some point or a Trojan horse that let them just walk in. What do most people these days do when they discover something like this has happened? Okay, aside from calling the guy they know who works in IT; what does he do? That’s right, he does a virus scan which targets things like that and removes them. So why not dig into the Norton archives and write some anti-Neo software? Sure, the Agents were basically anti-malware, but they really sucked at the job. If real computer viruses could be stopped by punches to the face, the hackers would have written anti-punch-in-the-face software and punch-back software. How about just identifying the code that sets off the warning bells and delete it? Presumably when they are in the Matrix, the people with the spikes in their skulls exist at least somewhat on the machine’s hardware. Now, the agents can’t take over people who have been unplugged. In the computer world, that means there is an obvious night and day difference between them, which means they should be easy for software to identify; not punchy kicky video game boss type software, the boring kind that no one ever sees. Hell, if they were clever enough, the machines could not only delete the intruders, but infect them back with programs that make them just shit everywhere and give their cohorts the bird.