I think that by the time this season ends, we're going to Lucy all grown up, quite deranged and set up to be far more of a threat than Murphy.
But will she still only have the mind of a child? Not if they follow up on that scene where Murphy eats Dr Merchs brain and gains her knowledge...
"Debating a troll is like trying to play chess with a pigeon..." — Modified Quote
That would require Murphy and his daughter to adopt full antagonist roles in the show's dynamic. I sure hope that this is not the case. I would much prefer that these two remain in a moral grey zone. I find this to be far more interesting as it adds depth to their characters.
I suppose it depends on the outcome of the next few episodes. As long as she's at the mercy of The Man, Lucy's first exposure to humans will have extremely negative connotations. If she is unfortunate enough to transfer directly from The Man's control to her father, she'll most likely adopt her father's hatred for mankind. However, if Warren and the others manage to get to her first, her personality could potentially develop positively, creating an opposition against Murphy.