Well, here we go again with unintended consequences... Since the Observers re-wrote the timeline so that Peter never existed, he never killed Jones. And I think everyone just assumed that Jones, as a Bad Guy, was in league with all the other Bad Guys on the Other Side, which apparently isn't the case. So I guess we'll have to see if Walternate figures out that his Broyles is a shapeshifter (presumably) before Altlivia and AltLee get themselves killed...
ETA: The "fall finale" became the "winter premiere"...? Nice try, FOX.