That plot twist was both heartwrenching and embarrassing to witness, hahah. Madoka finally takes the whole situation in her hands.
But I have to wonder. During the main story, when Sayaka was turned into a witch, Homura came to her rescue by stopping time and holding Kyouko's hand to keep her from being afflicted by the timestop. Does Homura do this by focusing her magic into her hands...or is it by simple skintouch? This would explain how Madoka wasn't stopped by time when she was being kissed, right?
Headcanon: This was how Homura figured out how her powers worked.