Nope, not joking. If "baggage" was an issue, then I suspect that teams would be far less accommodating of legal issues:
These are arrests, charges and citations of NFL players for crimes more serious than common traffic violations. Almost all of the players belonged to an NFL roster at the time of the incident. In rare cases, a free agent is included only if that player later signs with an NFL team. The data...
www.usatoday.com
If Kaepernick is a "mediocre" QB, then by definition he'd be better than half the league. Which seems about right; I certainly wouldn't put him anywhere close to the top tier, but he'd likely be a credible starting QB for one of the bottom-half teams, and would certainly be a quality backup.
Telling someone with whom we disagree to "live with the consequences" is pretty easy. It's a lot harder to apply that same principle when the time comes that it gets forced upon someone with whom we agree, and that time is going to come (or already has, as has been pointed out in the case of Tebow).
Once again, the NFL is a monopoly, and as such shouldn't be allowed to wield its power to censor employees in the same fashion as, say, the local fast-food joint.