From what little I could glean from the Internet, I got this:
A little Mercedes diesel engine info I found.
I can't find much information on the engine dimensions. IMO you will have height clearance issues as most inline diesels are tall engines. Is it turbocharged? You will have have better efficiency and power with a turbo. Win-win right there
You will need custom motor mounts and a custom adapter plate in order to install the engine and hook up the transmission. The transmission should be fine with the diesel, as long as it is not abused.
It is possible to do this swap. However! Are you expecting a quick Return On Investment, or are you wanting a custom high-mpg car and don't care about ROI? 60 mpg would not be out of the question with your overdrive, less weight and better aerodynamics.
I'm going to move your thread to Ecomodding Central so it will get more views. We have many knowledgeable diesel folks around here who can chime in. When and if you start, you can start a build thread and later explain in DIY/How-to how to swap this motor in a Civic.
Best of luck!