Fontaine had planned all along to have Jack kill Andrew Ryan, this is a given. However why string Jack along to Neptune's Bounty to save "Patrick and Moira"? What if Ryan had not blown up the submarine? Why take that risk? Sure you could say that "Atlas" wanted to gain Jack's trust but he hardly needed to, the game could have started with a "The man has gone mad I tell ya, if you want to get out Ryan is the only way, would you kindly go and get him to let us out of here by any means necessary?" or something like that... you know with more panache.