The original plan was to make it fairly cheaply, set in the present day of the 1970s rather than as a period piece, and to set it in either St Louis or Kansas City (I forget which one) rather than New York. The Paramount executives also wanted Ernest Borgnine to play Vito Corleone. It was on Francis Ford Coppola's insistence that they made it closer to the book and allowed Brando to do a screen test. The film was also originally meant to have less than a third of its final budget -- only $2 million -- but making it a period piece meant it became more expensive to make. So if you get rid of Coppola, you end up with a cheap, less-well-cast, poorly-adapted version of The Godfather which may simply end up being a bad movie.
How do you get rid of Coppola? Well, it may be easiest to simply prevent him from taking the job in the first place. And, if I recall correctly, there's a simple POD for that: don't let George Lucas convince him to take the job. Coppola was worried about selling out his artistic integrity and stuff like that but Lucas told him "Do the job now, get the cash and the credit, and you'll be able to do the stuff you want later." So, prevent that conversation from taking place and Coppola may pass on The Godfather.
After that, there are still ample opportunities for Coppola to drop out or be fired. His working relationship with the Paramount executives was infamously awful on that picture. But if you want to get rid of Coppola's effect on the film's artistic direction, then the earlier you get rid of him the better.
Now, actually making the film an outright flop will be difficult since it was only made for $6.5 million in OTL, and in the ATL may be even cheaper. But Paramount Pictures was in bad financial shape at the time and desperately needed The Godfather to be a hit -- so even if it ends up making a profit, it may still be regarded as a failure if it isn't enough of a success.