The real problem is, they're not very good at either right now. Yes the offensive line has looked embarrassingly bad in pass protection, but in fairness to those veteran players they're being asked to do things that aren't their strength nor have they been asked to do before (5 WR sets?). A good offensive line is not an absolute value, they don't operate in a vacuum. What line play works for a certain offense doesn't work for another and what was good for this team over the last three years clearly isn't good for them right now. Hulking, run-blocking guards and tackles are great for clearing lanes for your Hall-of-Fame tailback, not necessarily for keeping your Franchise Quarterback off his ass.
The 49ers could probably regain some form in the power running game with the players they have up front, rookie center Marcus Martin included, if they put their minds to it. But it's clear they don't think they can get over the championship-hump with that plan and they've got the wide receiver payroll to show it. It's also becoming clear that the team doesn't believe Frank has much punch left either. What clearer message could be sent by not handing off to him with the game on the line? Not once? With a timeout to burn?
So they can't (or won't) run and they can't throw with any kind of regularity. Therefore they can't score with regularity and obviously can't win with regularity.
I wrote before the opening weekend that this would be Harbaugh's finest season if he could pull off the transformation that was shaping up to take place, implementing all those flashy wideouts and diversifying the offense. It still could be, but the new territory he's pushed this team into looks as uncomfortable for him to navigate as it is for us to watch. Gone is the "bully" mentality and physical dominance that punctuated wins in the toughest environs. Now we have sloppy execution and last ditch efforts to come up short at home.
Perhaps the return of some familiar faces and some timely gifts from the defense by way of turnovers and field position will pull this team out of its funk. With as great as the defense can be, that's not an unrealistic scenario to play out, but it's obvious the offense has no blueprint to victory anymore. Not for the good teams, not for the bad teams. They're built to strike when the other team is on its heels, a regular occurrence when playing opposite a top 3 defense, but they're not built to dictate the pace of a game, not yet anyway.
They're figuring this approach out as they go and time is clearly running out for them to put it together. 10 points sure as hell won't get it done on the road against the Saints this week and 17 wouldn't either (for those of you convinced Kaep got in before fumbling). If there's a silver lining to this loss, it's that we're going to know exactly what this team is made out of going forward. A last second win would have taken some of the pressure and the stink off what's going on here. But with the loss there was no mistaking the gravity of the moment. This was either rock bottom, or the bottom is just falling out.