I think there will be a season long fall out. Lena is going to feel betrayed and considering the hang ups she has about her Luthor name, she is going to believe wrongly that not even her best friend trusts her because of her family.
That will take some work getting out of.
Rao I hope not. I realize that they will probably mine this situation for drama and Luther angst, but I hope they don't draw it out that long. Also if Lena does play the "it's because I'm a Luther" card, I hope that Kara points out that it was Lena that thought Lena was destined to be evil not, Kara.
Kara might also point out that she's good friends with Toyman's son, and that Kara's own Aunt and Uncle tried to enslave mankind.
Don't assume malice when stupidity is an adequate explanation. At least, not the first time.