From a momentum standpoint, yes, it is better to get hit by the bullet. From a kinetic energy standpoint, however, the bullet is going to be much more damaging since the energy is proportional to the velocity squared. However, the analogy holds up for energy, as well.
E = 0.5*m*v^2:
Baseball: E = 0.5*1*(95)^2 = 4512.5 (lb*miles^2)/hr^2
Lineman: E = 0.5*315*(10)^2 = 15,750 (lb*miles^2)/hr^2
I'm biased, but I've gotta go with Favre. I don't know Cal's injury history, but remember Favre played the better part of a season with a broken thumb on his throwing hand.
Good point about the velocity squared factor. It's why hs guys facing 75 are encouraged to "take one for the team" while pros facing 95 know that they better try to get out of the way. Nearly twice the energy to be absorbed at impact.
This leads to another point. While some incidents of HBP can be a glancing blow, many are direct impacts where the batter absorbs all of the kinetic energy in the ball. I really believe that it's a different situation when hitting the QB. Despite being encouraged to "accelerate through the tackle", the opposite usually occurs. The defender anticipates contact, braces for it, and actually ends up decelerating at the moment of contact.
There are other issues that diminish the effect of the collision in both cases. One is that an official baseball is between 5 and 5 1/4 oz rather than 1 lb. At the same time, there are not many 315 lbers that actually get to the QB. Most pass rushers are LBs or DEs in the 220 - 270 lb range. In addition, often a good portion of this mass does not impact the QB. Most tackles involve the defender supporting a portion of his own weight in a type of controlled fall. In many cases a OL is still hanging on to the defender and trying to impede his progress.
There are a whole host of kinesiology factors related to body movements that reduce the impact of the collision. QBs routinely bounce back up from a tackle from a 250 lb defender. You would have to pick up the pieces if they were hit with a 250 lb steel ball traveling the same speed.
It certainly wouldn't be fun to be the target of either a NFL tackler or an errant fast ball from someone like CC Sabathia. My choice would be to don pads and take on the hit, but others may certainly choose the other option.