It was extremely interconnected and allowed freedom through the restricted areas. A prison by definition would be restricted and controlling, not interconnected and would not allow much freedom of approaches.
Secondly, i could justify 47 smuggling in a gun and 2 pieces of equipment into a hospital, can't see that happening if we was a prisoner.
Thirdly, If he was a prisoner, then people would already know who he was, completely disregarding the whole "silent assassin" thing. "Oh look, this prisoner is called Tobias Reaper, and now he's missing and one of our wardens is dead".
Lastly, restrictive areas doesn't correlate to interesting "out of the box" thinking, like some people have suggested. Colorado and Marrakesh has big areas of restriction and both the school, consulate, and most of the outside area of Colorado were very bare in environmental and improvised kills. The same would be applicable to a prison setting.