You will have to decode the MPEG-2, find a filter that will filter out the stuff that bugs you, and then re-encode back to MPEG-2 before authoring a new DVD. Quite a lot of work there and you will lose a bit of quality in the re-encoding.
A good place to start is to download VirtualDubMod, this can read the MPEG-2 VOB files ripped from a DVD and has a selection of video filters built in.
For more detailed advice the two main sites to read are videohelp.com and doom9.org.