I think it is very possible that they are both BPA when the 49ers pick and would both add talent to the team. Assuming they go OT/OG with the 2nd then all that would mean is the team is choosing to outscore opponents next year instead of focusing on the D.
If you think you can add 10 pts. a game with Spiller getting 15 touches (plus return duties) AND having Bryant start in the Raye gun (really you might get 14 pts. more a game
), then you don't have to hold the opponent to so few points which would be the only explanation for not getting a pass rusher in the first 2 rounds.
But if they go Berry (pipedream he's there)/Graham/Huges/Haden etc. early then that means the D will be much improved next year and the offense will have to evolve with a mid to late round WR/RB. but need to score less and still win.
I'd personally go with plan A. Alex smith really looks like he can be special and if you give him Bryant to run mad and Spiller to take the dump off/screen to the house plus Davis, Crabs, Morgan/Hill/whoever, Walker, is mean that would be fun to watch.