I don't know, ominous music aside, that scene doesn't indicate she is going to go bad, if anything quite the opposite, as it shows Lena beating Lex at his own game. And she does so with a "White Knight". We are shown this flashback right after the scene where Lena tells Kara that she is her hero, or in other words Kara is Lena's White Knight.
But then there is that ominous music so...
One thing is certain Lena is a strategic thinker, and has enough patience to play the long game.
This post was created before that "chess scene". The addition of that moment changes some of the factors about this question.