I know what you're saying. Understand first that all elements of DVD VIDEO_TS structure are tightly integrated, including menus, thumbnails, audio, video, chapter points, etc. A change with any differences from the original structure and program points will likely make your DVD unplayable.
First, look at post #4. Decryption might likely be your first step. Afterward there are various demuxers that can separate VOB files into elementary video and audio streams, and there are many free audio cleanup apps. The revised audio is compressed back to AC3 or its original format by any number of free audio compressors and/or remuxers that can recompress the audio and join it to the video stream (it must be precisely the same bitrate, sampling rate, codec, and data size as the original), and make a new VOB.
ImagoMPEG-Muxer is one such remuxer. The linked website directory lists any number of decrypters and editors you could choose, with user comments and some guides:
http://www.videohelp.com/software. You can take your pick from any of dozens of apps for decryption, extraction and demuxing, etc. Obviously the high user ratings are the apps to pick. These apps and their interfaces constantly change, so user ratings are usually the best guide to reliability. It's not possible to guide you through every step using these softwares, but most of them are fairly easy to use and do rather limited but specific tasks.
So the basic steps are these:
a) decrypt if necessary.
DVD Decrypter or DVDFab can do this.
b) Use any app to move all files in the VIDEO_TS folder to your hard drive as VOB files (VOB2MPG is one such app that can do this, but the decrypters can also do it).
c) Demux audio and video into elementary streams. Some tools that can do this are
DVD Decrypter,
DGMPGDec, TSMuxer, TsDemux.
d) Revise your audio stream and recompress into its original format. The number of audio apps that can do this is too long to mention, but Audacity is a favorite as well as any of the muxer/demuxers already mentioned.
e) Join video and audio into new VOB's. Most of the same software in (c) can do this.
f) Make a new Video_TS folder with the iold menus and IFO files but with new VOB's, and burn to DVD.
g) Hope for the best.
Remember that you must go through each step for individual VOB program files, which begins with VTS_01_1.VOB.
http://www.videohelp.com/dvd#struct