They probably didn't want to detract from what obstensibly seems to be Weir's last appearance on the show. The "original" Weir is dead, as we discovered from the "nice" replicators, and I think it's safe to assume that the "copied" Weir is dead too, along with the rest of the duplicates. I agree completely. It made no sense for Sam to have been the one to have seen that vision, since it wasn't the real Atlantis that was destroyed, she wasn't duplicated, nor was she even mentioned in the episode. Some bad continuity by the writers.