In s1, Anya was acting on Lexa’s orders. The faceless commander was the antagonist BEFORE we knew that she was a lesbian, but it was still Lexa.
She was an antagonist (among others like Dante/Cage) in s2 as a foil for Clarke, proven when she betrayed her allies.
You could argue she was an antagonist (though to a lesser extent) in s3 for not letting the sky people have Mount Weather which became rightfully theirs when they conquered it without her.
Seriously, how much fanon does it take for you to think a character that regularly goes back on her promises (Mount Weather/not releasing Roan/reaffirming Clarke’s status as her prisoner in Hakeldama) and tried to murder 100 (UNARMED except for a single pistol until after they were attacked) children has never done anything wrong?