Remember, on one side, chemicals are to save children. On the other, Lena Luthor. Kara NEVER considers dropping her and saving kids. This tells a lot about their love.
The sad truth is that they only did this scene and one with Lena dedicating a statue to Supergirl to make their fallout worse towards the end of the season. All of this was to establish them as close and then the Reign and Kryptonite arguments happen and the cracks in their bond begins to form. They do the exact same thing in season 4 but in reverse. They have Lena borderline hating SG and then slowly getting close to her again only to rip it all out with Lex telling the secret.
