Yes the Fiat 2.0JTD is in fact a Peugeot/Citroen 2.0HDI engine.
If you get an HDI engine from a Scudo, Peugeot Expert or Citroen Dispatch/Jumpy of the same model, there should be no problem to swap the engine.
2.0HDI engines are also in the post 2007 model Scudo/Expert/Dispatch/Jumpy and in many other Peugeot and Citroen cars. It's possible that in those cases the wiring isn't the same as in a 2005 Scudo, so check that out before you start dismantling.