Joe, perhaps I’m not fully following your workflow, but where you say “But, this seems to create a problem as the original raw images will not remain untouched,” it’s not clear to me why that is a problem unless you want to always have available for reference right there in your catalog an undeveloped raw file. In my workflow, I’ll work on the raw file and thereafter, in most cases, never refer again to what it looked like “out of the camera.” If for some reason I want to see it in that original state, I can just make a virtual copy of whatever state the raw file is in at any point, and then fully reset that virtual copy. Then I have the virtual copy available for reference (or for a different approach to development) alongside the raw file in its current, developed state.
As for separate folders for your raw files and your output files, in my Lightroom catalog I have found it simplest in most cases to have all the files related to a given raw file in the same folder -- there are some exceptions that are, as Andrew alludes to, logical and useful for me but might not be for anyone else.
It seems that some reliance on keywords, smart collections, and develop module history states will help as you go forward.
My files are named only by the date taken and the image file number assigned by the camera. Most of my folders are named only by the date on which I imported the images from my card.
The videos of Tim Grey, available on Lynda.com or through his own website, have been useful to me from time to time and might be to you, too.