'Wireless' People Are Immune to Agent Takeover
The Agents cannot enter the mind of someone who has hacked in - so far as the system knows, they don't exist. The people who hack in (Neo and the rest of Zion's crews) are isolated from the Matrix's governing mind. All interactions with them are done in-Matrix, via actual dialog, rather than the way the Agents talk to each other/the Matrix core (exemplified by their ear pieces).
The reasoning for this is fairly simple: People who are wired in to the Matrix are directly connected to the Matrix's core code. The Matrix has root for them, in security parlance. It can be aware of anything they experience (or have experienced and recall) and can change/alter/control their bodies and perceptions.
In this manner, Agents can take over the bodies of people during emergencies. They are Agents of the system, which inserts them into compatible locations ('blue pill' humans).
Zion's hackers, on the other hand, do NOT have a direct connection to the Matrix core code or processes. Rather, they exist within the construct of the Matrix and interact with it. The Matrix becomes aware of them only when their interactions stray into the controlling AI's notice. Lacking direct access to their minds, the Agents cannot access them to take over.
Thanks to Neo injecting himself into Agent Smith's code, Smith gained some of the powers of the One - he exemplified this by being stronger and faster than even the upgraded agents and by overwriting his code into others by touch. The most likely explanation is that Agent Smith, using the knowledge and power he gained from Neo, altered his (now-useless due to disconnection from the central Matrix core) overwriting code so that he could copy (instead of cut & paste) by touch. Instead of what the other Agents do (which presumably permits them to cleanly exit a person, removing their memory of being taken over) he obliterates the person and copies his personality and appearance onto their form.
When he put himself into Bane, he overwrote Bane's mind with his own, allowing him to propagate into the real world. This was possible ONLY due to the changes he had undergone thanks to Neo's actions at the end of The Matrix. Standard Agents cannot do this, or they would have simply overwritten Zion's crews at every opportunity (and Smith would have simply overwritten Morpheus when he was captured - if he gained the Oracle's eyes and was able to pass as Bane for a period, it's reasonable to suppose he retained access to the person's memories).