It seems that throughout the season we have seen Jessi struggling with who she is and fighting her 'programming' it seems like she has broken free from her program because she no longer believes the life story that was fed to her. So if she has succeeded in breaking free and is now just a confused kid, as Kyle once was, why would she betray Kyle like her programming told her to? Brainwashing should only be effective when you are unaware it is in place; as a function of the subconcious brain, once it moves into the stream of conscious thought it is no longer in control of our decisions. Its like when you are doing something out of habit/reflex, like riding your bike or blinking; you don't take any conscious thought to consider what you are doing. But if you become aware of what you are doing and begin to focus on your actions they are no longer automatic and may even begin to seem strange to you. So now that Jessi's subconscious programming has been moved into her conscious thought it would seem unlikely that she "couldn't help [herself]", as she told Kyle when he asked her why she had taken the information from his mind. So the question is did she do it out of programming or because she feels that helping Madacorp is the only way for her to be free like Emily promised her? Also, if she did it on purpose why did she feel guilty enough afterwards to jump over the falls; did she do it just to make a quick escape and get the info back to Madacorp?
One more question, away from the topic of Jessi, is why would the house appear as if no one had lived there for a long time? Baylin is obviously in no condition to monitor his equipment and take care of the necessary functions himself, so someone would have to be around, and the house would be the only place for them to be when they aren't with Baylin. My guess is that Tom Foss is the one who has been taking care of Baylin. This is based on the facts that A)Baylin told Kyle the ring was all he needed, and told Kyle that he knew where he needed to go, so Foss must have known about the cabin already, and B)I think this must be where/why Foss disappeared for so long when he left Kyle alone, in order to check on Baylin.
Unfortunately we have to wait awhile to find the answers to these questions....all I can say is at least it isn't as bad as LOST :)