The writers did a poor job of wrapping up Crisis, especially with the stupid "Lex is awesome" rewrite of the Book of Destiny. However, Lena remembers the original history, so her interactions with Kara from original Earth affect her choices now, instead of the patched together post-Crisis history.
The Lena arc is similar to the Rosenbaum Lex Luthor arc on Smallville. They start out being honestly good people trying to make up for the bad name of Luthor, then suddenly become villains because they didn't get praised enough for their efforts. Coddling Lena wasn't working. Kara needed to tell her she was on the wrong path.