I think she was absorbed by the Golden Marker just when the Necromorphs reached the Psychiatry Wing of the Hospital into the Sprawl; she was ONE of the Marker's five makers, of course (Patient 3). But I'm not sure about her true fate... o.O
She was immune to the Red Marker's Last Shard (seen in Dead Space: Aftermath) and therefore IMMUNE to the Site 12 Marker withal, but due to the lobotomy she suffered at the hands of the Overseer's Personnel, Isabel was vulnerable to the Sprawl's Marker. D=
I do hope, notwithstanding, that some charitative soul carried her to a shuttle and make her left the Sprawl safely. C:
In Dead Space 3, EarthGov was completely destroyed by Unitology. So it's possible that The Church Of Unitology had sent their agents to evacuate Isabel Cho from The Sprawl before it's outbreak and destruction in Dead Space 2. And later on used as proof to expose EarthGov's corruption which would be their ultimate downfall!
I believe she was "tried" by a kangaroo court and sentenced to death even before the Sprawl outbreak. Every protagonist that dies in the series had his death implied, but not shown entirely. This was just some kind of policy from EA, probably to create speculations that they may have survived and make the endings seen less frustrating (while it's obivious they didn't have a real chance).