I would rip the VOBs, truncate with mpgtx (don't know if it supports VOB though), concat (with [color=blue]cat[/cololr] in the Terminal but I think mpgtx can do that too), and author a new DVD image (I know DVDSP can, I think Sizzle or ffmpegX can. If any of those don't like VOB you can demux to m2v/whatever audio it uses probably mp2 or pcm with bbDemux).
the other option is to completely decode the whole thing to mov, edit (anywhere, but QTPro will be easiest), and recode it back to MPEG2. This will definitely work, but will take forever and the quality will be seriously degraded