Remember back in the Mike Sherman days when teams dared the Packers to beat them with Favre? Brett's abilities were being mocked by the rest of the league, and for good reason, his play had gone down hill for quite a few years. McCarthy came in and changed things. I'll grant that McCarthy was a no-nonsense coach who put Favre on the leash that he always thrived under. However, he brought out one of Favre's best seasons in 2007 - possibly better than his MVP years. He's now turned Rodgers into arguable one of the greatest in recent decades, and has teams drooling over his backup (Flynn). Nobody wanted Flynn for the same reasons some of you are throwing around about Harrell. He came from a completely different system, his college stats (and national championship) mean diddly in the NFL, etc.
Don't discount how little work the 3rd string QB gets beyond getting to run the scout team. Harrell is also younger than Flynn so not having the offseason hurt Harrell's development more than Flynn's. If any coach deserves our trust in scouting and training a QB, it's McCarthy.