I remember reading a thread on the Westeros boards about this. I don't remember the passage from the book myself, but apparently the council of duders that handle the contracts for the Faceless Men will not send the assassins after people they knew in their first lives. That said, I think it's very likely that Arya will finish her training and then be all "Fuck ya'll, I'm outie" for one reason or another.
One thing that was brought up though, is that Arya knows Sansa - she doesn't know Alayne Stone. So there is theoretical potential for her to be sent after Alayne Stone, find out it's Sansa in trouble, kill Littlefinger. That could be how and why she ends up leaving the Faceless Men.
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