if Neo and others live in pods
I think this is the part that requires correction.
Neo, Morpheus, Trinity, and the whole group of "freed" humans living in Zion means they are no longer part of the Matrix. This means agents/machines can not just unplug or
just reset, press delete or rewrite the code to get rid of them
Because these humans don't connect to Matrix via the same routes as machines do via pods etc. They kind of hack into the Matrix, even there is a dialogue in the movie where Morpheus tells Neo that they hack into the Matrix so that they convince humans to literally wake up from the Matrix, which is why the Architect designed agents to hunt down humans like Morpheus because they created hindrance in their master plan and machines can not simply unplug them or reset or delete them.
Neo, in the beginning, is part of the Matrix i.e. living in a pod, and therefore it was easy for agents to get rid of him but they didn't choose to because they wanted to capture Morpheus.