Since Madoka herself employs Familiars as the supreme goddess of the world, then we can't consider Familiars or Witches as evil, they are just another state of existence. Extrapolating that, we pretty much end up with 'since Madoka removed all despair and regrets from dead Megucas, they are in full control of their soul, both its good and bad parts'. This pretty much leads straight into the idea that there are very rare Magucas (like Kirika) who are able to accept their fate as a Witch and control it fully because they feel no despair whatsoever. Kirika was able to control her Witch form, as a normal Puella Magi (she still died to turn into a Witch though), because she had fully accepted and embraced exactly who she was and what she was going to become. When you think about it, and this was proven by Kirika in the Oriko spin-off, a Witch goes out of control due to a mix of unacceptance and of it being your darker traits put into the light. That means that they are able to control their darker halves without falling into despair (or even requiring despair). Dead Megucas like herself and Nagisa are at peace with their souls.

Get out of that jabroni outfit