Grant Cohn: Cut him or keep him? 49ers' Colin Kaepernick decision will come from top

SANTA CLARA - Both of these statements probably are true:

1. Chip Kelly wants to keep Colin Kaepernick on the 49ers' roster this season.

2. The 49ers don't want to keep Kaepernick on the roster this season - in fact, they might get rid of him before the season even begins.

Those statements may seem to contradict each other but they don't. Kelly explained why at his press conference Tuesday morning.

A reporter asked if the Niners have discussed cutting Kaepernick. “No,” Kelly fibbed. “We've been kind of on track with what we've done. We knew we were not going to release any quarterbacks at the cut to 75, so we haven't had a discussion about the quarterback position at all.”

Translation: “We discuss the quarterback position every day. Management wants to cut Kaepernick and I want to keep him. We argue constantly.”

“Is Kaepernick one of your best two quarterbacks right now?” A reporter asked.

“Yes,” Kelly said, and left it at that. Meaning Kaepernick merits a spot on the roster and Kelly wants to keep him as the backup quarterback, maybe even as the starter down the line.

The reporter asked a follow-up question. “If (keeping Kaepernick) strictly were a football decision and it were up to you … ”

“It's not up to me,” Kelly interrupted. “Any decisions on this team are made through everybody. I don't have control of the 53-man roster. I don't sit there and say, ‘This is the 53 we're picking.' It's a group effort.”

To clarify what he meant, I asked, “Exactly how much say do you have over who makes the final roster?

“The final say is Trent's (general manager Trent Baalke),” Kelly explained, “and that's the way it should be. But it's not like I can say, ‘Hey, I like these eight guys,' and he's like, ‘I don't care about those eight guys; we're going this way.' I think we've got a real cooperative relationship as we're handling the team moving forward. And I think the one thing about it is we see things the same way in terms of how to build a football team.”

Translation: “We don't see things the same way at all. In a sense, I'm at Baalke's mercy. I can't stop him if he wants to cut Kaepernick, or if Jed York wants to cut Kaepernick. All I can do is tell the media I consider him one of the two best quarterbacks on my team. Then the media can infer that Baalke overruled me if Kaepernick gets cut.”

It's easy to understand why Kelly would want Kaepernick as the backup. The alternative is Jeff Driskel, a rookie sixth-round pick. At least Kaepernick has NFL experience.

What's difficult to understand is why 49ers' management would want to cut Kaepernick in the first place. Why would they get rid of their second-best quarterback when their starter isn't particularly good? Almost no one expects Blaine Gabbert to make it through the whole season without getting benched or injured. So the backup probably will have to play eventually. Shouldn't the backup be Kaepernick?

From the 49ers' perspective, the answer is “no.”

I'll explain.

Say Kaepernick starts the season as the backup. He could become the starter by midseason and suffer an injury that requires surgery. Then, he could put off the surgery for a few months like he did last season just to make sure he can't pass a physical on April 1, 2017. That way, his $14.5 million base salary next season becomes fully guaranteed.

That is Jed York's worst nightmare. He may be thinking Kaepernick already stole $11.9 million from the Niners this year whether or not he makes the team. Letting Kaepernick steal another $14.5 million next year is out of the question and just bad business.

The only way York would want to pay Kaepernick all that money is if he earns the starting job this year and plays well, which he hasn't done and probably won't do.

Here's what York probably told Kelly during the quarterback discussion Kelly alleges never happened: “As you know, Chip, Trent is in charge of our 53-man roster. But you have some control as well. You get to choose which players start. We'll keep anyone you decide is a starter, even if it's Colin Kaepernick.

“But if you DON'T start Colin, then you don't get to decide whether to keep him. Then it becomes an organizational decision, and I run this organization. And I say we cut Kaepernick.”

One thing complicates this already complicated issue, Kaepernick refusing to stand for the national anthem. If the 49ers cut Kaepernick, some people will say the Niners cut him because of that. Bad optic, as they say, for the Niners. But the 49ers have a valid response, one York must have worked out already. The 49ers can say with absolute truth that they have supported Kaepernick's right as an American to sit during the anthem and to complain about the United States. The 49ers have supported him. They even issued a news release supporting him. They are in the clear.

Here's what's going to happen. The 49ers will wait until after the Chargers preseason game on Thursday. If Kaepernick plays poorly, which he probably will, they will cut him for his bad performance.

End of story. End of Kaepernick around here.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat's website. You can reach him at grantcohn@gmail.com.