That perhaps is the biggest question entering Sunday's season-opening showdown.
Packers linebacker Clay Matthews believes the defense can take its shots at Kaepernick, treating him as if were a running back when he's running the read-option scheme that tormented Green Bay's defense in the playoff game, particularly in the second half.
San Francisco coach Jim Harbaugh believes otherwise.
Speaking on ESPN Radio on Tuesday, Matthews said: "One of the things that the referees have told us is that when these quarterbacks carry out the fakes, they lose their right as a quarterback, a pocket-passing quarterback, the protection of a quarterback. So, with that, you do have to take your shots on the quarterback, and obviously they're too important to their offense. If that means they pull them out of that type of offense and make them run a traditional, drop-back, pocket-style offense, I think that's exactly what we're going for. So, you want to put hits as early and often on the quarterback and make them uncomfortable."
How the officials judge it could play a role in the 49ers' play-calling.
Based on Packers coach Mike McCarthy's conversations with the NFL's officiating staff dating to their visits in the spring, McCarthy on Thursday said he has a "strong understanding of how we're going to approach the game."
That understanding, McCarthy said, will show up in the Packers' game plan.
"The reality is, the quarterback is part of the option," McCarthy said. "There's three options, obviously: the quarterback, the dive and the pitch. The ability to go tackle that player is obviously within the rules."
Speaking at his locker on Thursday, Matthews had little else to say on the subject. He said the team understands the rules, but is there any gray area, given the league's preference for protecting its passers?
"We'll find out," Matthews said. "The natural progression of the game with quarterbacks who continue the play-fake, we'll see. But we feel good about our scheme and what we're going to try to accomplish up there."
Asked on Wednesday about the rules pertaining to the quarterback, Harbaugh told 49ers beat reporters on Wednesday: "Before (the quarterback is) declared being a runner, then he should be afforded the protection that all quarterbacks are afforded, until he declares and gets out of the pocket and starts running with the ball or running an option or carrying out a bootleg and attempting a run or pass when he's outside of the pocket. But, while he's in the pocket I believe that he's a quarterback until he declares that he's a runner. I think that those are the conversations right now. I haven't gotten final clarification on what it's going to be."
Harbaugh took it a step further, using the word "targeting" pertaining to Matthews' "tough talk" about hitting Kaepernick. That brings to mind intentionally trying to injure a player and the entire can of worms of the Saints' bounty program.
"You definitely start to wonder," Harbaugh said. "A man will usually tell you his bad intentions if you just listen. You know what's being said publicly, not what's being said privately. You hope that their intent isn't going to be anything that's not within the rules."
The report was unchanged from Wednesday.
"Jarrett Bush is the special teams captain. That's how we view him," McCarthy said, confident that Bush would be ready for Sunday. "He sets the tempo over there for us. Very productive football player. I'm not used to having him on the injury report."
49ers: Did not participate: RB LaMichael James (knee). Limited: CB Nnamdi Asomugha (collarbone).
As was the case for Green Bay, San Francisco's report was unchanged.
-- Special teams coordinator Shawn Slocum said he had not decided who will return kickoffs and punts, nor has he decided whether Mason Crosby or Tim Masthay will handle the kickoffs. Randall Cobb has not been ruled out of returns, Slocum said. Jeremy Ross is in the mix for both jobs, as is Micah Hyde on punt returns and Johnathan Franklin on kickoff returns.
-- Rather than lock up with the opponent's No. 1 receiver, as he did last season, Tramon Williams will line up at left cornerback and Sam Shields at right cornerback. "It kind of works out better for the defense when you can do it that way," Williams said. "Guys won't know where guys are on the field. Certain things like that, when you know guys are matching, you know where he's going to be on the field. Quarterbacks tend to know where to go with the ball, so I think it's going to work out better."
-- McCarthy put the team through a padded practice on Thursday, which emphasized fundamentals. McCarthy called the team periods "clean."
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Bill Huber is publisher of Packer Report magazine and PackerReport.com and has written for Packer Report since 1997. E-mail him at email@example.com, or leave him a question in Packer Report's subscribers-only Packers Pro Club forum. Find Bill on Twitter at twitter.com/PackerReport.