I would go for magic, may I ask what powersets your gonna take?
To me:
Natural = normal for the species. If you're playing an animal, for instance, and pick powers similar to attributes the animal would have in real life (i.e. claws), they can be put down to being of natural origin.
Magic = a normal species with powers unnatural to them, but acheived through an artifact or ritual or similar.
That said, I have a character with a similar backstory - her powers are normal to her species, but she was brought to Paragon/life through a magical ritual, hence her origin is Magic. Though, I could have also quite easily chosen Natural origin and made reference to the ritual which brought her into being.
Both can work brilliantly. Though, I would suggest that if you want her to have access to magic-esque powers, or at least an ability to perform magic, I'd pick Magic. If you're keeping her exactly as was, and only making reference to Balaaj's ritual, Natural will do.
Magic: A Natural being useing Unnatural/Non Natural/Supernatural Powers can also be Aplied too Demons Because Most of them Know atleast the Basics of It (hence Why Most Mages Summon them, To tap that Knowledge)
Natural: if She is Something Different then Human (or even Still human) Now and Can Use Abilities That Are Better or the Same as humanity. She could still use Magic too an Amount but her Abilities are Part of her being.
Example, I have had a Fey as a Character she Was Natural in Origin, even thou she was a Creature of Magic, Tao'Grim my Main Villian is Magic in Origin Even thou she is a Demon and Hence a Creature of Magic, most of her Abilitys are Natural too her but she Also can Cast Magic and Wants too learn more of it
Not sure if this is helpful or not but Balaaj is actually natural, heh. She's a demon so her powers are natural for her. I believe the resurrection of Eres will actually give her some honest to god powers (rather than commanding mercs and using devices and traps), so that would be magic?
At least that's how my brain works through it. Eressos is still a human with no innate abilities at all, and got her abilities (and resurrection) through magical means. Meanwhile there's no class of "newly revived" that is expected to have certain powers so can't really be natural.
Thanks for the feedback so far guys; mulling it all over in my head at the moment.
As for powers...I was originally tempted to go Something/Thermal Corrupter, but Augury just pointed out to me that Mercenaries/Dark would be just as thematic - keeps with her original "main" power, but also gives the mystic edge. Eres' mercenaries were loyal guys after all, so it stands to reason they'd come back to her.
I'll plan it a little more before setting anything down, however. Thanks again. 
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Mercenaries/Dark would be just as thematic - keeps with her original "main" power, but also gives the mystic edge. Eres' mercenaries were loyal guys after all, so it stands to reason they'd come back to her.
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Keep her as a mastermind sure, although I was having an idea about the primary...
Since her 'boys' have been through (in effect) hell and back with her, they could be Thugs instead? That'd portray the whole "tough, hardy, wily" so and so's whose normal military style equipment have degraded from overuse but still they follow their leader! Still keep the same names maybe?
Dark of course is just awesome, secondary and rpness-wise.
And yeah I'd say Magic Origin..
Chiefette
Meanwhile a character of mine would be Going the Oppisite Direction.. Rickman My mm, Would be Drilling and Instructing his "Lads" in getting Better in there Disipline.
Sorry of-topic..
Just a little something I've been tossing around lately....
Due to my old Mastermind, Eres, snuffing it in a - as of yet anyway - unwritten story (OOCly it was due to the account going poof, wah), I'm tempted to use this as a nifty chance for more Roleplay and an extended narrative.
Problem is, I'm unsure of what Origin she should go for.
She started out as Natural - lead a group of mercenaries, over time becoming heavily augmented (Joined with Black Scorpion's faction in the end), and probably would have gone so far as to jack herself into one of the Spider Bots if it hadn't been for death. Regardless....
Her partner-in-crime (and possibly more. Unresolved sexual tension ftw) Balaaj, just happens to be a Demon, and just happens to know some people who know some people that can do the whole "dig up the soul and shove it in a new body" routine. This is where it gets difficult.
Would her Origin still count as Natural, as that's where her story began? Or would she have made the leap to Magical, due to her "new" powers manifesting due to Balaaj's tampering?
It's not a massive thing, but the Origin tab is still big enough to nibble at the back of my mind.