The first thing that sticks out there is that the build of FFmpeg is horribly outdated. There could very well have been improvements in libavcodec's MPEG-2 encoder over the past two years. There's certainly commits to the MPEG-2 encoder that have occurred in that timeframe, but I can't tell you if/how much it's impacted the quality. I use HCenc for MPEG-2 encoding (even on Linux and OSX, by using Wine), not FFmpeg.
What is the exact problem with the output video? Macroblocking or mosquito noise? Sub-par deinterlacing or inverse telecine? Blurriness of some sort?
The things I can suggest as possibilities:
It looks like the audio there is already compliant with DVD. Just demux it with FFmpeg:
and save it until the end. You don't want to introduce any generation loss there, plus the original bitrate is lower (256kbps) than the one the conversion you were doing was using (448kbps) - which just wastes space for no benefit. Converting the audio to a higher bitrate from a lower one won't get any quality back.
ffmpeg -i 00030.MTS -vn -acodec copy 00030.MTS.ac3
Scenario 1: Fully native
A) Rebuild FFmpeg from current git. Make sure to use --enable-avisynth when configuring it. Really, do this no matter whether you go with scenario 1 or 2 - it's a good idea regardless.
B) Build and install AvxSynth (the build instructions there are outdated in regard to FFmpeg and FFMS2; it can use the git versions of both of them).
C) Use AvxSynth to do the deinterlace/inverse telecine (probably using Decomb, aka Telecide/Decimate, since that actually got ported to AvxSynth, albeit for 64-bit only apparently) and resizing to 720x480.
D) Give the script to FFmpeg and encode:
Scenario 2: With Wine
ffmpeg -i input.avs -i 00030.MTS.ac3 [mpeg2 options] -acodec copy 00030.MTS.mpg
A) Get a recent build of FFmpeg for Windows from http://ffmpeg.zeranoe.com/builds/ and stick it in Wine's PATH
B) Install AviSynth+. AviSynth 2.6 alpha 5 is also an option if avsplus' installer fails to properly install under Wine (you can then take the zipped version of avsplus and replace 2.6a5's avisynth.dll with the one from avsplus). If Wine hasn't been updated to take advantage of VS2012-built stuff (which the official builds of avsplus require), then you can just stick with 2.6a5.
C) Use the greater supply of deinterlace/inverse telecine filters for normal AviSynth to do the processing, along with other types of filtering if desired, and resize to 720x480.
D1) Use HCenc 0.26 (under Wine) to encode to MPEG-2, and mplex (part of MJPEGTools, it's in the repositories) to mux the output .m2v and .ac3 files together:
mplex -f8 -V 00030.MTS.m2v 00030.MTS.ac3 -o 00030.MTS.mpg
D2) Use the Windows build of FFmpeg to do the conversion like before.
D3) Use the Windows build of FFmpeg to pipe out of Wine to the native build of FFmpeg:
wine ffmpeg -i input.avs -f yuv4mpegpipe - | ffmpeg -i - [rest of options] output.mpg