Why should they necessarily? When the plug is a control mechanism the logical conclusion would be indeed to simply destroy the plug or destroy the connection of it to the EVA.
The problem is it was never realy explained how the plug works together with the Unit. I would guess Nerv and Seele aren't stupid and built the Eva's in a way that makes them reliant on the plug to operate.
But that begs the question how 'going Berserk' works. In the show we are being told it's the implanted Soul taking over control. That would suggest there is a way to bypass the plug completely.
On the other side we are talking of a 100 meter somewhat cyborg with cybernetics and stuff. These would need to be controlled by a computer system to open the pylons for example or the spike launcher of Unit02.
The plug, I think, also interprets the neural data and then sends it towards the Unit. And with being human-like, it would need to control body functions like breathing, swallowing or that almost uselees digestive system the Units have.
In the end we simply don't know how most of the things work. That leaves us only to say 'Black Magic' or 'science'.