While I've been confused by Sanctuary before, the decision to air "Uprising" after "Tempus" really had me scratching my head. The way the two episodes did play out left little mystery. From "Tempus" we knew Magnus was perfectly safe and would reappear shortly after disappearing. Indeed, she shows up at the end of the episode, as expect, and saves the day. There's nothing surprising about that, and it's actually a bit boring.
On the other hand, if the episodes were flipped, there would be plenty of confusion over Magnus's whereabouts, and her arrival would actually be a twist. Then, the next episode would be "Tempus," explaining how Magnus got back. It would allow the cliffhanger at the end of the third season to be stretched an extra episode.
As for "Uprising" itself, it's the usual Sanctuary resolution to a big problem. First, there are the implications that it will be the end of the world if the characters don't save the day, and then the characters do save the day. There are some deaths and disruption, but the world is not changed irrevocably. At this point, we can expect Sanctuary not to go for any major game changer.