How big are consequences for 49ers if they cut Colin Kaepernick?

·NFL columnist

A week ago, Colin Kaepernick’s future represented a football problem for the San Francisco 49ers. Today, it’s a little more difficult. The quarterback’s national anthem protest has put the organization at a complicated crossroads, where the realities of salary, performance, protest and optics all merge into the same lane.

Now the 49ers have less than a week to choose a direction with Kaepernick. And it likely won’t be appealing – whether he remains on the roster or not.

While the NFL landscape surrounding Kaepernick’s protest has been filled with support and condemnation, the stance on his football career is a little less debatable. Kaepernick has continued slipping. And the 49ers noticed this long before his national anthem protests became a national lightning rod. Even before Kaepernick’s anthem stance, two personnel sources told Yahoo Sports the quarterback wasn’t making the progress hoped for in coach Chip Kelly’s offense. While there was no clarity offered on the 49ers potentially cutting Kaepernick, the bottom line was clear: The optimism of Kelly’s offense successfully rebooting the quarterback’s career had developed considerable doubts.

Colin Kaepernick might not make the 49ers' 53-man roster. (AP)
Colin Kaepernick might not make the 49ers’ 53-man roster. (AP)

Had football been the only factor, the thought of the 49ers releasing Kaepernick was problematic enough. It would come after an offseason when San Francisco had motivating factors to cut ties with the quarterback at least twice: once via a weeks-long trade dalliance with the Denver Broncos; another via a contract deadline that would have allowed the 49ers to cut Kaepernick before April 1 and void his $11.9 million base salary for this season.

But rather than cut him loose, the 49ers kept Kaepernick in the fold, hoping Kelly’s offense would resurrect a player who led the franchise to the Super Bowl after the 2012 season. This despite Kaepernick demanding a trade in the offseason and a locker room that had already seemingly embraced Blaine Gabbert as the team’s starting quarterback.

Keeping Kaepernick – and paying him – seemed to make it a virtual certainty that he would be in San Francisco for at least one more season. But the sources indicated there has been some frustration with Kaepernick’s progress since the offseason activities began. A large part of the problem has been his seemingly continual physical limitations due to nagging injuries. The 49ers hoped he would dive into the offseason with renewed vigor under Kelly, who offered him a clean slate. Instead, he missed the most rigorous portions of the offseason program and never gained the necessary traction to persistently challenge Gabbert for the starting job.

As the preseason whittled away, those realities started to make another factor more pressing. Specifically, the terms of Kaepernick’s deal call for a career-ending injury to lock in prearranged salary guarantees. If Kaepernick suffers a career-ending injury this season, the 49ers are on the hook for $19.7 million in guaranteed salaries ($14.5 million in 2017 and $5.2 million in 2018). But there’s a rub that works in the team’s favor: As part of his deal, Kaepernick purchased an insurance policy that awards $20 million to the 49ers in the event of such an injury. In essence, the 49ers are covered even if Kaepernick’s career comes to a sudden catastrophic end.

That insurance policy was supposed to take some of the risk out of the later stages of Kaepernick’s contract, making it more palatable to retain him, even if he was relegated to backup status. But the contract also contains offset language, which means the 49ers could cut him loose and not be held responsible for an amount matching whatever another team pays him. Should he be released and land a $3 million contract elsewhere, the 49ers save not only that money, but also avoid a $1.125 million roster bonus that kicks in when the 53-man rosters are finalized on Saturday.

The 49ers' final preseason game is on Thursday in San Diego. (AP)
The 49ers’ final preseason game is on Thursday in San Diego. (AP)

So the 49ers have financial protection to keep Kaepernick. But there is also some financial incentive to release him. What couldn’t be foreseen in all this contract planning was the protest twist, which adds another element of drama to the equation. While the 49ers have stated their support for Kaepernick’s stance, there is an underlying reality that exists for virtually every NFL team (aside from maybe the Dallas Cowboys). Most front offices and coaching staffs attempt to practice drama-avoidance when it comes to a team’s makeup. While exceptions happen for exceptional players, backups are rarely afforded significant breaks. And right now, Kaepernick is a seemingly fading backup who has lingering physical issues and future salaries that don’t match his contributions. Teams rarely go out of their way to accommodate players like that.

This is where the 49ers run into a mess of converging issues. While Kaepernick’s football state and future salaries would suggest a departure is the wisest choice, there is now an optics problem. While the team would surely suggest cutting Kaepernick is a football-only decision, there will be no shortage of skeptics who suggest the move is related to his protest or social views. It also doesn’t help that Kelly suffered criticism from NFL players in the past, over such roster decisions as the retention of Philadelphia Eagles wideout Riley Cooper (after he used a racial epithet) and the jettisoning of LeSean McCoy, who condemned Kelly’s relationship with black players.

Laid out on the table are options that NFL teams typically seek to avoid. One is keeping Kaepernick despite knowing the franchise may experience continued media distraction from a regressing backup player who isn’t in the long-term plans. Another is cutting Kaepernick loose and enduring the inevitable criticism that his anthem stance must have played a role in the decision.

San Francisco has only a few days to make that decision. And it likely won’t get any easier as the deadline draws closer.