But we don't know what exactly happens when Madoka saves them. Maybe saving means that they don't become witches, but still change, like how Sayaka and Bebe did. They do disappear after Madoka picks them up after all.
Homura became a witch because she was isolated with a barrier. It has nothing to do with her wanting to become one.
If you mean at the end when she grabbed Madoka, she was already a witch, and at that point surpassed Madoka in power, thus enabling Homura to steal part of Madoka.