Given the scientific resurrection capabilities we have witnessed in the Stargate Universe from seemingly less advanced races that couldn't create a planet, to make a mistake or oversight of that caliber seems unreasonable. Even if they had some non-interference directive that precluded allowing lasting life to already dead people; forcing all of the Faith planet colonists to go through the horror of dying a second time while Destiny's crew had to stand by and watch helplessly was imo rather pointless and even cruel.
JM's blog suggests that the writers would have us believe that it was an unfortunate mistake on the part of the aliens. I think the writers wanted to introduce a new shuttle and tie up the Faith planet storyline. The episode imo came across as contrived and in line with SGU's penchant for depressing and melodramatic storytelling.