Well, here are your options.
Option 1: Start Colin Kaepernick. This is the most obvious choice, and likely what the coaching staff has in mind. There's no guarantee that it will work out, though. 49ers fans like to talk about Kaepernick like he's destined to be The Future, but its worth noting that mid-round signal callers rarely turn out to be elite players. Thirty eight quarterbacks have been taken in 2nd, 3rd, or 4th round of the draft in the last ten years -- and between them there have been a total of only 2 Pro Bowl appearances (by Matt Schaub and David Garrard, neither of which are elite QBs).
You can see the list for yourself. Outside of Andy Dalton, Matt Schaub, David Garrard, and possibly Kyle Orton, this is a list of terrible quarterbacks. More than half have never been a week 1 starter, and only eight have started for multiple seasons. Does this mean Kaepernick is destined to be terrible? Of course not, but he's definitely not guaranteed to be any good.
Option 3: Draft a new QB. Despite what Bleacher Report may tell us, it's a little early to be projecting the first round of the 2013 draft. 7 weeks into the season, though, I think we can make some general statements about which teams will be in the hunt for a new quarterback come draft day, and roughly where they will end up in terms of draft order. There have been a ton of quarterbacks taken in the past few years, so there are only a handful of teams who could afford to take one early next season. Here are my guesses:
So what does this tell us? For one thing, all of the teams definitely looking for a QB will likely finish with a higher draft pick than the 49ers. Anything can happen, of course. But the Chiefs look done, the Cardinals are about to face one of the toughest schedules in all of football, and the Jets are a sideshow. I don't think 10 wins is likely for any of these teams.
Given that these teams will also have more draft capital than the 49ers to trade up, the 49ers will, at best, be able to get the 4th best QB in the draft. Its too early in the college season to say who that is, but here's who the 49ers would have gotten in the same position over the last 10 years.
Again, Harbaugh and Baalke might be able to work some magic and find their own Andrew Luck in the middle of the first round. But history is not on their side.
Option 4: Go after a current NFL QB. Here's my list of definite, possible, and trade-worthy free agent QBs.
Option 4a: Sign Joe Flacco. The unibrowed bomber will likely be the best QB on the market come 2013, as long as Baltimore doesn't lock him up before the end of this season. Downsides: He's inconsistent, he whines to the media a lot, and he's going to be much more expensive than Alex Smith. But damn, that dude can throw a pretty deep ball. He's shown that he has the ability to manage his team through successful seasons, even when facing some of the toughest defenses in football. The 49ers have a better offensive coaching staff and arguably better offensive personnel, so Flacco should be able to find success with the 49ers.
Option 4b: Sign Michael Vick after the Eagles inevitably cut him. Is Vick, at 32, reaching the twilight of his career? Probably. Does he have issues with accuracy and reading defenses, as well as a newfound talent for fumbling in the worst situations? Absolutely. And is he one of the most injury prone QBs in the league? You bet. But you have to admit that the prospect of combining the 49ers' league-leading running game with Michael Vick, one of the best scramblers and deep ball passers ever to play the game, is tantalizing. Vick, who's been shoehorned into a west coast offense in Philadelphia, is clearly not suited for dropping back 40-50 times a game and moving the chains with 7-10 yard YAC passes against complex defenses. In San Francisco, all he would be asked to do is throw 20-30 passes a game, with Roman's formations simplifying defenses for him. We'll see how the season goes, but its definitely possible that Vick ends up garnering a contract about the same size as Alex Smith's. He's definitely worth "evaluating," as Harbaugh would say.
Option 4c: Sign or trade for a young prospect. Specifically, I'm talking about Matt Flynn, Nick Foles, Joe Webb, Kirk Cousins, Chase Daniel, Tyler Thigpen, and the like. Honestly, no one can say definitively how good any of these guys are. Flynn and Foles are the (relatively) big names here, while Webb and Thigpen are the kind of dual run-pass threats that Harbaugh seems to like.
Option 4d: Sign or trade for a game manager with some upside. Matt Hasselbeck, Colt McCoy, Jason Campbell, Matt Moore, etc. This is what I like to call the "meh" option. Hasselbeck is likely the best out of this group, but why would the team trade Smith for an older version of Smith?
Option 4e: Sign Tim Tebow. LOLOLOLOLOL