Ok, I have tried a few things now and this is the only work around I can come up with right now. I installed the XYtools plugin from the python plugin repository. I also installed the xlrd and xlwt python modules. From their I converted my csv file to xls using libreoffice calc. After installing XYtools you should see it in the vector operations menu and I import the xls file into QGIS as a using the ," Open Excel file as attribute table or point layer " option. I make my adjustments to the file as necessary. ( for my test I tried adding some points and deleting some points with the editing tools ) Then I used the field calculator to update the x and y fields in the layer so it reflects the position of the changes and then I save the edits and remove the file from the map canvas. The changes are updated in the xls file.
I know this is not exactly what you were looking for, however it is the best work around I can come up with that will allow you to work on a file in a simple format and save everything to a single file. I think bringing this issue to the attention of the QGIS devs is probably the best course of action to get a real solution to this issue.