Many believed that Kaepernick was going to be released anyway had he not voluntarily removed himself from the roster and, in an interview with Mike Florio of Pro Football Talk, 49ers GM John Lynch confirmed as much.
"Yes, and we had that conversation with him. So I don't want to characterize it as he made a decision to leave here. We both sat down and under that current construct of his deal, it was a big number," Lynch said. "Kyle [Shanahan] had a vision for what he wanted to do, and one thing I think Kyle was very clear and I think Colin appreciated, is that Kyle has an idea of how he'd play with Colin Kaepernick. But he preferred to run the exact offense that he ran in Atlanta last year that was record-breaking in this league. And if you change it for the quarterback, you change it for everybody on that offense. So he had a great discussion that I think gave Colin clarity, so we moved on.
"Brian Hoyer was one of the guys we pursued. Once we pursued him, we didn't see Kap as a backup that would really fit in that scheme and we communicated that to him. So I think we've been very up front with it. But I think that is a fair characterization. Yes, he was not going to be here under the construct of his contract. We gave him the option: 'You can opt out, we can release you, whatever.' And he chose to opt out, but that was just a formality."
Lynch. And he continued that trend when he addressed a report that stemmed from Peter King of TheMMQB.com saying some folks with the 49ers believed Kaepernick might prefer social activism to playing football; Lynch said he regrets that the "perception" of the 49ers "contributing" to that viewpoint of Kaepernick was out there.
In fact, Lynch said that Kaepernick struck him as someone who wants to play football "at the highest level" again.
"I feel like that's part of my job is controlling what comes out of this building, and to the extent that there was a perception that we were contributing to that Colin didn't want to play football, we wanted to put an end to that," Lynch said. "I've talked with Colin and I've told him that I felt bad that if indeed that is contributing to that thought. The one thing that I knew from sitting with Colin when we had our opportunity to sit down and he ultimately opted out, we had a great discussion that stuck out with me that this is a guy who is really interested in getting back in this league and playing at the highest level. And I've talked to him since, and that very much is the case."
The Kaepernick situation is a fascinating one, because there is no one definite reason why he hasn't landed a job yet. He would be a major upgrade for multiple teams in terms of their backup situation from a pure talent standpoint, but he also brings a lot of media attention, something that NFL teams do not crave when it comes to backup quarterbacks.
There are absolutely scenarios where Kaepernick's activism is costing him a chance at work, too; it would be naive to believe that every single team out there is perfectly fine with, even if he's already said he .
Let us also be clear: much of Kaepernick's activism has been extremely positive. He also helped to provide food and water for the people of Somalia, donated a huge sneaker collection to charity and gave Meals on Wheels a $50,000 donation., a positive thing for society. Kaepernick has