TL;DR

SID単位でStreamを分離
data streamの除去
再エンコードは行わない

上記のようなことを行うスクリプト

#!/bin/sh
SID="$1"
INPUT="$2"
OUTPUT="$3"
exec avconv -i "$INPUT" -map p:"$SID" -map -d -codec copy "$OUTPUT"

avprobe

変換前

$ avprobe 'hoge.ts'
avprobe version 11.7-6:11.7-1~deb8u1, Copyright (c) 2007-2016 the Libav developers
  built on Jun 12 2016 21:51:35 with gcc 4.9.2 (Debian 4.9.2-10)
Input #0, mpegts, from 'hoge.m2ts':
  Duration: 00:30:00.95, start: 15279.402967, bitrate: 14618 kb/s
  Program 23608
    Metadata:
      service_name    : ▒▒▒▒▒!!▒ر
      service_provider:
    Stream #0.0[0x111]: Video: mpeg2video (Main), yuv420p, 1440x1080 [PAR 4:3 DAR 16:9], 20000 kb/s, 29.97 fps, 90k tbn, 59.94 tbc
    Stream #0.1[0x112]: Audio: aac, 48000 Hz, stereo, fltp, 243 kb/s
    Stream #0.2[0x740]: Data: [13][0][0][0] / 0x000D
    Stream #0.3[0x750]: Data: [13][0][0][0] / 0x000D
    Stream #0.4[0x751]: Data: [13][0][0][0] / 0x000D
    Stream #0.5[0x752]: Data: [13][0][0][0] / 0x000D
    Stream #0.6[0x960]: Data: [13][0][0][0] / 0x000D
    Stream #0.7[0x961]: Data: [13][0][0][0] / 0x000D
    Stream #0.8[0x75e]: Data: [13][0][0][0] / 0x000D
    Stream #0.9[0x75f]: Data: [13][0][0][0] / 0x000D
    Stream #0.10[0x96e]: Data: [13][0][0][0] / 0x000D
  Program 23610
    Metadata:
      service_name    : ▒▒▒▒▒!!▒ز
      service_provider:
    Stream #0.12[0x131]: Video: mpeg2video (Main), yuv420p, 720x480 [PAR 32:27 DAR 16:9], 15000 kb/s, 29.97 fps, 90k tbn, 59.94 tbc
    Stream #0.11[0x132]: Audio: aac, 48000 Hz, stereo, fltp, 255 kb/s
    Stream #0.13[0x840]: Data: [13][0][0][0] / 0x000D
    Stream #0.3[0x750]: Data: [13][0][0][0] / 0x000D
    Stream #0.4[0x751]: Data: [13][0][0][0] / 0x000D
    Stream #0.5[0x752]: Data: [13][0][0][0] / 0x000D
    Stream #0.6[0x960]: Data: [13][0][0][0] / 0x000D
    Stream #0.7[0x961]: Data: [13][0][0][0] / 0x000D
    Stream #0.14[0x85e]: Data: [13][0][0][0] / 0x000D
    Stream #0.15[0x85f]: Data: [13][0][0][0] / 0x000D
    Stream #0.10[0x96e]: Data: [13][0][0][0] / 0x000D
  Program 23609
    Metadata:
      service_name    : ▒▒▒▒▒!!▒ر
      service_provider:
    Stream #0.0[0x111]: Video: mpeg2video (Main), yuv420p, 1440x1080 [PAR 4:3 DAR 16:9], 20000 kb/s, 29.97 fps, 90k tbn, 59.94 tbc
    Stream #0.1[0x112]: Audio: aac, 48000 Hz, stereo, fltp, 243 kb/s
    Stream #0.2[0x740]: Data: [13][0][0][0] / 0x000D
    Stream #0.3[0x750]: Data: [13][0][0][0] / 0x000D
    Stream #0.4[0x751]: Data: [13][0][0][0] / 0x000D
    Stream #0.5[0x752]: Data: [13][0][0][0] / 0x000D
    Stream #0.6[0x960]: Data: [13][0][0][0] / 0x000D
    Stream #0.7[0x961]: Data: [13][0][0][0] / 0x000D
    Stream #0.8[0x75e]: Data: [13][0][0][0] / 0x000D
    Stream #0.9[0x75f]: Data: [13][0][0][0] / 0x000D
    Stream #0.10[0x96e]: Data: [13][0][0][0] / 0x000D
  Program 23992
    Metadata:
      service_name    : ▒▒▒▒▒
      service_provider:
    Stream #0.17[0x281]: Video: h264 (Constrained Baseline), yuv420p, 320x180, 10 fps, 90k tbn, 29.97 tbc
    Stream #0.16[0x283]: Audio: aac, 48000 Hz, stereo, fltp, 30 kb/s
    Stream #0.18[0x780]: Data: [13][0][0][0] / 0x000D
    Stream #0.19[0x789]: Data: [13][0][0][0] / 0x000D
    Stream #0.20[0x98a]: Data: [13][0][0][0] / 0x000D
    Stream #0.21[0x98b]: Data: [13][0][0][0] / 0x000D
  Program 23993
    Metadata:
      service_name    : ▒▒▒▒▒
      service_provider:
    Stream #0.22[0x381]: Video: h264 (Constrained Baseline), yuv420p, 320x180, 14.99 fps, 90k tbn, 29.97 tbc
    Stream #0.23[0x383]: Audio: aac, 48000 Hz, stereo, fltp, 29 kb/s
    Stream #0.24[0x880]: Data: [13][0][0][0] / 0x000D
    Stream #0.25[0x889]: Data: [13][0][0][0] / 0x000D
    Stream #0.20[0x98a]: Data: [13][0][0][0] / 0x000D
    Stream #0.21[0x98b]: Data: [13][0][0][0] / 0x000D
  Program 23615
    Metadata:
      service_name    : ▒▒▒▒▒!!▒▒NW;~
      service_provider:
Unsupported codec with id 0 for input stream 2
Unsupported codec with id 0 for input stream 3
Unsupported codec with id 0 for input stream 4
Unsupported codec with id 0 for input stream 5
Unsupported codec with id 0 for input stream 6
Unsupported codec with id 0 for input stream 7
Unsupported codec with id 0 for input stream 8
Unsupported codec with id 0 for input stream 9
Unsupported codec with id 0 for input stream 10
Unsupported codec with id 0 for input stream 13
Unsupported codec with id 0 for input stream 14
Unsupported codec with id 0 for input stream 15
Unsupported codec with id 0 for input stream 18
Unsupported codec with id 0 for input stream 19
Unsupported codec with id 0 for input stream 20
Unsupported codec with id 0 for input stream 21
Unsupported codec with id 0 for input stream 24
Unsupported codec with id 0 for input stream 25
# avprobe output

SID:23608を取り出しデータstreamを除去する

変換後

$ avprobe fuga.mp4
avprobe version 11.7-6:11.7-1~deb8u1, Copyright (c) 2007-2016 the Libav developers
  built on Jun 12 2016 21:51:35 with gcc 4.9.2 (Debian 4.9.2-10)
[mov,mp4,m4a,3gp,3g2,mj2 @ 0x8f6d00] multiple edit list entries, a/v desync might occur, patch welcome
[mov,mp4,m4a,3gp,3g2,mj2 @ 0x8f6d00] multiple edit list entries, a/v desync might occur, patch welcome
[aac @ 0x8f8660] channel element 3.5 is not allocated
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'fuga.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 512
    compatible_brands: isomiso2mp41
    encoder         : Lavf56.1.0
  Duration: 00:30:00.55, start: 0.014000, bitrate: 8601 kb/s
    Stream #0.0(und): Video: mpeg2video (Main), yuv420p, 1440x1080 [PAR 4:3 DAR 16:9], 20000 kb/s, 29.97 fps, 90k tbn, 59.94 tbc (default)
    Stream #0.1(und): Audio: aac, 48000 Hz, stereo, fltp, 255 kb/s (default)
# avprobe output