Is it a factory 200Tdi or a conversion?
Which part of the side panel. If you mean behind the rear well, then you'll have to ditch the rear silencer, although you could relocate it. If you mean between the door and rear wheel arch. Then you'll either have to straight pipe it or completely custom fab up a silencer. Both likely to increase noise, the one by the door more so. Esp if you have the windows down.
Also worth noting that cutting a hole in the body tub is a one way mod. You won't be able to easily 'undo' it.