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I don't think Jessi ran away to get Kyle to follow her to his
impending doom. I actually think she's genuinely afraid of what
she is, and of what she thinks she may be. The fact that she didn't know
any of her background as being a weapon suggests that Madacorp is
also trying to keep that information [for whatever reason] away from
Jessi. If they wanted a cold-blooded killer who hacks into other clones'
memories, they would allow her that capability. I do think, however, that
by imprinting a "human" personality into Jessi's memory, Madacorp
has created the fear she feels now over what she has done. I'm nearly
certain that with enough memory exploration [via the help of Kyle],
she will have the capability of choosing whether or not she wants to return
to her former self. The issue therein lies in the fact that she is
programmed to remove the information from Kyle's memory, and
would likely choose to continue her wayward lifestyle.

Speaking of that, is Jessi supposed to remove Zzyxx
files from Kyle's memory, or is she only supposed to obtain
them? I haven't quite figured that out yet. I know Madacorp wants
the information "at any cost", but I don't remember seeing anything about
whether it's okay for Kyle to keep [as a "backup" or something]. I've
come to the realization that Madacorp is uninterested whether or not
the "source" of the information is destroyed. Though it seems to me that
they would want a second "soldier" on their side; someone they can control
[awkwardly enough, like they do Jessi].

In regards to Emily, once she finds out about what Madacorp
is hiding, I think she'll want to be a more important figurehead in the
company; I don't think she'll leave [or even betray] Madacorp. I do
think that she will look for Jessi out of fear for her life, out of fear for
her daughter's life, and out of fear for Jessi's life. She's been in this
role of "big sister" for so long now, that she's starting to think of Jessi
almost as a daughter figure. Such is evident in the way she punishes
Jessi for some of her behaviors.