Well, all you really need is one of those splitter/joiner pieces of software. However, I'm not really aware of one that can do both at the same time AND works well.
What I can suggest takes two programs, from the same company. It'll cost $60 total to buy them both. The Boilsoft AVI/MPEG/RM/WMV Joiner and the Boilsoft AVI/MPEG/ASF/WMV Splitter. See http://www.boilsoft.com
I have these. I use them to split or join files. I've never done what you want (before my test, that is), but it'll work.
It's akin to the old-fashioned way of using TMPGEnc MPEG TOOLS to edit an MPEG file. You'd have to split each segment into a file, cutting out the "good stuff" between commercials. Then use the joiner to join all the segments.
I'm not aware of any freeware for this. I think all the splitters/joiners charge money. Most AVI software is for editing and re-encodes, so the terms to use while searching would be "splitter" and/or "joiner" and not "editor".
I tested out a ATI MMC HuffYUV
capture, and did a split, then a re-join or the split segments. It was fine.