Levi said exactly that. Make your own decision. Eren initially wanted to transform, but instead, he got convinced by the pleadingeyes of his team. He should have followed through and believed in both Levi's advice and himself.

I understand that she is a noob, but she has more than proven what she is capable of during the last attack. Moreover, she is ALWAYS running after Eren and not following orders. Why not just place them together? A better commander would have taken that in consideration and ignored the usual process and placed the proper people in the proper places. It was an understandable decision to group Mikasa with the other new recruits, but it wasn't the best.