Gary Andersen just walked away from $12M at oregon State University because he felt (according to his statements) it the principled thing to do. That is highly admireable.
Kaepernick's protest was of a different sort, I think. Using a poor analogy, he didn't walk away from his job as a fry cook at Mcdonalds because he wasn't getting the burgers done correctly, he protested sonething having nothing to do with his emloyer, in his workplace, while at work, perhaps damaging his employer's brand (treating the dinner table like a toilet), and then complains that his employer essentially fired him. I am not sure that is quite admireable.
I don't quite buy that Kaepernick was willing to walk away from mountains of cash. If so, then why file suit when the NFL obliges. If he was so willing, then I think you're right.
Mostly, I think CK overplayed his hand. He QB'ed a team to the Super Bowl once, It seems that he thought he was thusly guaranteed employment, regardless of his on-field behavior.
There isn't anything much that allows you to seperate Kaepernick from a Tyrod Taylor or Trevor Siemian. Given that, why hire him when other replacement parts are available.