The short version, and this is a problem that occurs with many, many DVD sets, is that CBS/Paramount didn't have anyone who was intimately familiar with these music cues, and didn't go outside to consult with the people who do know who wrote which cue.
But here's the rub: No matter how complicated this may have seemed to the executives at CBS/Paramount, the action they took – ruining one of the all-time classic TV dramas – was unnecessary. There are experts in Los Angeles who are intimately familiar with this music, among them music editor Ken Wilhoit, who performed all that detective work in the first place. And he's not the only one.
These people can instantly spot a Herrmann cue versus a Goldsmith cue, and could, with a few weeks and a little effort, correctly identify every piece of music in the second season of The Fugitive. And those very few Capitol cues in dispute could easily be removed and replaced by generic music, salvaging the vast majority of original score for fans to enjoy.
This happens a lot, doesn't it? Studios frequently release shows with episodes out of order, cut versions included by mistake, music replaced that wouldn't actually cost the studio anything -- mistakes that die-hard fans of these shows could spot instantly.