Hypothetically (because I don't know if Agatha was in Crystalized), how would she react to Golden Oni Lloyd ? You know, the very angry boi who went psycho on the Overlord ?

I think she'd behave the same way she does in the novel: when she sees Lloyd in this state, she's very frightened and afraid to approach him for the first few minutes, but quickly pulls herself together and decides to confront him. Trying to calm him down and remind him who he really is, dodging his attacks (if he acts like in that scene when he kicked the cage doors and attacked Harumi). In short, she'll be scared to death of him, but knowing real Lloyd, she can't leave him like that and will do everything she can to get him back in control.

And yes, Agatha is present throughout the seasons, it's just that her first appearance is in "Future of the Past" since all the events surrounding her take place in the far corners of the Ninjago world :)