I think it's pretty clear the writers intended for Jacob's brother to be the smoke monster. The episode is billed as explaining "Locke's motivations." If the smoke monster is merely taking the form of Jacob's brother and the form of Locke, then the episode failed in this, because the smoke monster didn't appear until the final five minutes of the episode, and there is no explanation about it or its motivations. We learn a lot about Jacob's brother and his motivations, though; if he merely died and his form was adopted by the smoke monster, it seems a waste to delve into his character. That's just from the storytelling standpoint.
Within the actual story itself, we're told that the brothers cannot hurt each other, hence the necessity of the loophole. The smoke monster tells Richard that Jacob took "[his] body, [his] humanity." Jacob's brother wants to go home; the smoke monster tells Ben it wants what John Locke didn't: to go home.
And in an interview I read with Lindelof and Cuse today, Cuse says:
"We wanted to explain why the Man in Black had behaved the way that he does, and to show that like a lot of other characters on the show, he's the victim of very bad parenting. To reduce him to just a supernatural force, as opposed to a person, was not our intent. "Across the Sea" was our attempt to say, "Here's why Jacob feels the way he does about people, why the Man in Black feels the way he does about people," and a bit about their childhood. It's as simple as that and as complex as the themes of the show are."
http://www.hitfix.com/blogs/whats-alan-watching/posts/exclusive-interview-lost-producers-damon-lindelof-and-carlton-cuse-talk-across-the-seaIt just doesn't seem to make much sense to me to try to separate the smoke monster and Jacob's brother into separate entities. It's needlessly complex, and really makes the episode worse, because the episode is about Jacob and his brother; the smoke monster doesn't figure into it as a separate entity, and if it were a separate entity, the episode offers zero insight into its motivations or purpose. Something bad happened to Jacob's brother when he was thrown into the light by Jacob, and now he's the smoke monster.
Poll