Supposition: Mike Peterson is in a room controlled by shield, not centipede. We know they just crashed a bunch of labs and took much of 'pede's technology. Why WOULDN'T they try and build themselves a super soldier who was forced to obey?
Alternate supposition: Parts of shield have been running Centipede all along. This makes less sense, but might still work.
Alternate supposition: Parts of shield have been running Centipede all along. This makes less sense, but might still work.