@guess:
I like this theory on Kuma and his bible. I think its very interesting but I do have some theories of my own that I'd like to share.
I have a feeling that now that Kuma is a robot his bible works as some kind of programing. Kinda how the real bible can be thought of as a guide book on how to live your life. I think that Kuma and Dragon wrote the original program, but like any program it can be updated. I think that dragon has the ability to alter the program. Kuma only went along with the experiments to accomplish the objectives of the revolutionary army, and as long as those objectives are written in the bible, he will be able to continue accomplishing those objectives. I think that although under the orders of Vegapunk and the marines, the orders of the revolutionary army override come first. In this way Kuma may have been willing to go along with the process; knowing that although he would lose his humanity, he would in this way be able to hold on to his own will (not a free one, but his own). It would also make him quite the martyr, which goes with the whole christian motif. Iva and Luffy were attacked at Marineford because the bible codes only work on PX0, and not the other pacifistas. Also i believe that when Kuma appeared in SA, he sent the ship, shakky and the fishy trio off to a safe place.
time will tell
i wud erally hope that kuma toook the ship away from them, and they demonstrate their strength by storming into marinesford together to get their boat back