What we do know is that Newt was in love with her, and according to David Yates, he’s still in love with her.
He goes on to describe her as “damaged and confused” and very much having a power over Newt.
Yates also confirmed that we’ll see Leta Lestrange in the second film.
The fact that he calls her a “tragic figure,” added to what Newt says about her not fitting in at school makes me think it would be too big an assumption to paint Leta as an all-out villain, or even assume she’s to blame for Newt’s expulsion in some way.