Speculah:The War Between Good Guys Theory
This theory suggests that both the witches and the magical girls believe themselves to be the "good guys." The conflict isn't good versus evil, but rather two groups of good guys fighting for their own methods of saving the world or due to misunderstandings.
Witches Trapped in Illusion
Witches may perceive reality differently, through hallucinations or insanity, and think that they are the magical girls fighting against monsters. They never realize that those "monsters" are actual magical girls.
Hitomi's reference to "going to a wonderful world together" in episode 4 suggests that witches attack normal people in order to "rescue" them. These people might turn into the minions that populate the barrier.
The official website's cards for Elsa Maria, Sebastians, and Kriemhild Gretchen support this interpretation. The cards state that Sebastians are an aggregate of lives that have been saved by Elsa Maria, and that Elsa Maria is self-righteous, prays for all life, and tries to bring all life into her shadow. Kriemhild Gretchen is stated to be the witch of salvation who endeavors to make heaven a reality, and will not stop working to save everyone until the world is completely free of misfortune.
The spinoff manga Mahou Shoujo Kazumi Magica: The Innocent Malice might actually be featuring a witch. She lost her memories and wakes up to find herself in the form of a magical girl. It's possible that this is an illusion, and she's actually one of the witches the real magical girls will fight.
Witches Fighting for Revolution
The witches are former magical girls who believe that the world is inherently corrupt. They've realized that all use of magic will inevitably lead to the creation of evil forces. They're trying to recreate and purify the world in order to raise heaven from the ashes of Earth. They think that magical girls are only prolonging humanity's suffering in a flawed world.
Madoka will eventually be forced to choose a side. She must either defeat the witches and seal away the power that creates them, allowing humanity to stand on its own, or become the witches' leader and bring about the creation of a new world where everyone can be happy, but at the cost of destroying the existing world.
Kyubey may actually be on the witches' side. He understands the dangers of magic and hates having to endlessly send magical girls to their deaths, but some spell or curse forces him to follow his assigned role and keep his mouth shut. He's trying to find a magical girl who will turn into a witch powerful enough to break the cycle.
This theory can be combined with The Global Reset Theory: Madoka chose to compromise by restarting the world the way it was, giving everyone a second chance, but with premonitions or subconscious memories in dreams to help them fix the mistakes and regrets of their previous lives. The show could be taking place in this recreated world.