Whatever it is that should have happened to Shepard's body doesn't matter, because it's stated explicitly in the dialogue between the scientist and TIM that Shepard's brain was kept largely intact (apparently Shepard was wearing the same magic helmet Elmer Fudd had). The realities of prolonged exposure to space and the physical trauma of falling from orbit were tossed out the window for sake of creative license.
There's really no use trying to wrap logic around Project Lazarus, because it basically goes nowhere. Without so much as a hint in the story about the details regarding Shepard's reconstruction, I can just as well assume that it's simply quick and convenient technomagic that serves as an easy way to get Shepard to work with Cerberus, and that if BioWare's intention was to have reaper-manufactured hardware be involved in the Project, they would not beat around the bush with vague details, especially not when other characters that are derived from technology taken directly from a reaper or the Collectors are made clear on this point immediately. Given that Mass Effect's internal logic is anything but airtight, word of god would be a requirement for this point.
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