The backup/starter (and money that comes along with it) conundrum has been my general explanation so far. He’s better than most backups, but the indication was that he wanted a chance to be a starter (and, to be paid like someone with a chance to be a starter). I generally think the distraction thing is silly, but for a backup QB, you really don’t want them to be paid a lot of attention unless they’re playing.
Since starters have been going down, he definitely seems the best pick, though. He may not be a very good starter, but he’s a legitimate one, and if you put a decent team around him he can get you to 2–2 (or better) in the absence of your starter. There’s something to be said if his salary demands are too high (I can’t say what they are), but besides that I’d definitely take him over RGIII or Cutler.
Kind of weak, in my opinion, on the part of the owners. A few babies might protest, but, again, people protested Ray Rice. Most of them will get over it. Do what you think is right. Fact is, Kaepernick did nothing wrong — he exercised his right to free speech.