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Okay, scratch what I said before about Mami.

 Spoiler

Went back a bit. Mami's gem is on her hat (or in her hair, whatever), which Charlotte targeted first. All that drops from Charlotte when she dies is a hunk of flesh (which is probably from Charlotte exploding), a cup of tea, and the Grief Seed. Homura picks up the seed. It's not shown much, but what Homura picks up doesn't have the flower on top of it like Mami's gem, and it has a different enclosure that Mami's gem.

So, considering the witch went for Mami's head first, it's probably safe to assume that they know about a the soul being separate from the body. and specifically went for the soul first. So yeah, Mami's probably just 100% dead.

EDIT:

BY THE WAY, IF THERE'S ANYONE THAT'S STILL A BIT IN DOUBT ABOUT EPISODE 3 OF MADOKA, HERE'S THE SCENE IN THE MANGA

 Spoiler

And before anyone asks, the manga is based off the anime, not the other way around. There's also supposed to be a spinoff manga at the end of the series. There's also another manga that's following 3 different magical girls, and it's called Puella Magi Kazumi Magica ～the innocent malice～, but I don't know much about that one. http://www.dokidokivisual.com/madokamagica/kazumi/