Sure, there’s a slight chance that Jacob could have been an honest person who only got looped into the big conspiracy at a more recent period, it’s highly unlikely, since Jacob has only come off as a smarmy and too-understanding schmuck, and not a nervous nelly.
Jacob could very easily have been manipulating her for all the years that they have been together, and possibly before.
Sarah Wayne Callies basically echoed what I (and presumably lots of other viewers) thought as soon as Jacob was seen in those final minutes, being a little too friendly and chatty with the two potentially deadly threats.
Immediately, everything we thought we knew about Sara’s life went right out the window, since there are no guarantees that anything that has occurred in her life happened because of her best intentions.