There's also the chance of major ****storm, once everyone figures out that Shepard was rebuilt using reaper technology...
Hold up, hold up. What's your source for that?
To clarify the subsequent conversation, etc.: there is not, to this date, any official source for this possibility. I was speaking in a possible direction where the script of ME3 could go, pure speculation on my part.
As far as ME2 is concerned, only two "friendlies" have reaper technologies embebbed in them. The first is TIM himself, with his husk eyes, and the second is EDI, which was built using reaper tech (ME2: "it appears my design includes hardware recovered from the wreckage of sovereign") - perhaps that's what Ravenholme was remembering.