Echoes of <i>All My Sins Remembered</i>.
I haven't read this book, but Joe Haldeman's amazing classic also has an involuntary surgically altered superspy with implanted personalities, who over time starts doubting that he's on the right side.
(Come to think of it, it's a bit odd that Hollywood hasn't made a movie adaptation of AMSR yet. Could be a great sci-fi Bourne-like action vehicle. But on the other hand they'd probably butcher it, I, Robot style.)