Sam Koch is the one who calls that fake. Harbaugh has said in the past that anytime Sam reads the defense loaded up to try and block it from the offense's right, he has the option of jogging it in from the left. We've done it twice in two years and both times it looked identical and was executed perfectly.
Further, the idea that running the fake could lead to cheap shots by the Raiders can be dismissed entirely by the fact that they picked up their FOURTH personal foul for late hits or face masking on that drive. They were already cheap shotting. That TD was our response. (My dad and I both predicted something like it when Curry picked up his second late hit penalty. As soon as it happened we looked at each other and said that Flacco was going to go back to the hurry up and bomb them into submission to teach them a lesson.)
Maybe it can also be payback for them pulling awful trades that fave our enemies free draft picks (Patriots and Bengals) and free Randy Moss's (Patriots).