Lena never fully abandoned Kara, she wanted to, but couldn't. The moment she realized Lex was working against Kara she ran to her apartment, threw herself at Kara's mercy, and begged to help her. Did she do all of this for the greater good? No. She did it because in that moment Kara's safety mattered more to her than anger, revenge, or ego. The show made it clear that every time Kara was in danger Lena was willing to put everything aside to protect her. When push came to shove she cried as she chose not to send the email to Andrea that would have exposed Kara, this kept Kara safe. She had the chance to escape with Myriad while Kara was fighting in the fortress, she risked her own goals to help protect Kara, once shaikh choosing Kara's safety over her own. She had a panic attack when the Kryptonite cannons almost shot Kara, once again Kara's safety came first. She cried and almost broke when she saw the pain she caused by using Kryptonite on Kara in the fortress. It's clear, Lena would never abandon Kara, she was literally incapable of it.
Lena never fully abandoned Kara, she wanted to, but couldn't. The moment she realized Lex was working against Kara she ran to her apartment, threw herself at Kara's mercy, and begged to help her. Did she do all of this for the greater good? No. She did it because in that moment Kara's safety mattered more to her than anger, revenge, or ego. The show made it clear that every time Kara was in danger Lena was willing to put everything aside to protect her. When push came to shove she cried as she chose not to send the email to Andrea that would have exposed Kara, this kept Kara safe. She had the chance to escape with Myriad while Kara was fighting in the fortress, she risked her own goals to help protect Kara, once shaikh choosing Kara's safety over her own. She had a panic attack when the Kryptonite cannons almost shot Kara, once again Kara's safety came first. She cried and almost broke when she saw the pain she caused by using Kryptonite on Kara in the fortress. It's clear, Lena would never abandon Kara, she was literally incapable of it.