The Red Pill was likely just an "avatar" of what was malware that attacked the hardware of the pods that the connected people were in and prevented a virtual death from actually killing the target.
As such, it was highly-specialized for its sole task.
When one of the crew sneaks back into the Matrix, however, it's not the hardware on the Nebuchadnezzar that is the problem. It's the systems that it connects to, that can't be manipulated into "telling" the person that they've woken up from the Matrix. And they may have no malware that can attack those systems, or perhaps the person has to be processed by specific nodes for the "awakening" thing to happen (regardless of whether the humans had gotten root on the nodes currently being used).
There are many things that are apparently possible within the Matrix that even Neo never learns to do: for instance, with all the evidence of non-mundane spatial geometries, why was Neo never able to teleport? Certainly it would be as simple as rooting some computer node or another, and overwriting his location with different x,y,z coordinates. In the same way, they must have not had access to tell the relevant computer node to release its connection to the human, at which point they could safely be removed from the simulation.