Baker is just redundant. He's likely never going to start a game at 2nd again this year so the only at bats he'll get will be at 3rd when Aramis needa a day off. I'd rather sub Aramis with a Tracy against a righty since Tracy has proven in the past to hit rhp fairly well.
Baker will get more pinch-hit at-bats though. He's the only right-handed player off the bench when the Cubs face a left-handed starter (except for Hill who doesn't really count in a pinch hitting discussion). Baker can also play all over the field which gives Lou more options to work around with his other players.
The Cubs also have more left-handed players that need to be replaced with a right-hander for certain at-bats against LOOGY's, so it's good to have 2 good right-handed bats on the bench. 3 left-handed bats on the bench is pretty redundant because the only player that needs to be substituted for if a right-hander on the mound is Baker. Since Tracy is the 3rd of those left-handed batters, it's unlikely the pitcher's spot is going to come up 3 times and need pinch-hitters.
So yes, Tracy is likely a slightly better backup to Aramis, but Baker beats him in every other area.
Not to mention the fact that Tracy is already down in Iowa. If the Cubs need him in case of an Aramis injury, he can be called back up. If Baker leaves, the Cubs might not be able to keep him. And if Theriot or Castro gets hurt, the Cubs will want Baker as an option.