I think I misread your post if you are talking about coupling the Magnaflow kit components with 2.5" piping. Those components may not work with that size piping, but I'm not 100%. Going with 2.5" and removing the cat, would require a full custom build, or long-tube headers and one of the available 2.5" setups.
The only real issue is the possibility of beginning to run a lean AFR, though there isn't a lot of data showing of just how lean the system will/can get. Focusboy is running the long-tube headers and his dyno did show a slightly lean condition, though still within tolerances. Obviously, waiting for a tune is always the best option.
FocusFest 2013: Best of Show
Gateway FFW: Show Class Outstanding
September '13 ROTM
Hatch Nation #161