Why would Michael want the money back? He used it to bribe the Vatican so he could get a controlling interest in Immobiliare.
Better part of a billion $(!) is way too huge for any bribe and Michael already had to officially pay for the Immobiliare stocks, no? By comparison, Howard Hughes' whole estate at the time of his death in 1976 was 2.6 billion $ and he was one of the richest men of his time.
The new Pope had already ratified the deal so his goal was accomplished. It never occured to me that the bank got bust too.
Well, the bank was in trouble already, which is why they needed Michael's (massive) deposits. And if the bank didn't go bust, why did Keinszig run? This whole segment is modelled on Banko Ambrosiano crash isn't it?
Of course, the idea of the Bank of Vatican going bankrupt is fairly ludicrous, which doesn't help this plot one bit.
Nor does it make any sense for Corleones to murder Keinszig. His RL counterpart was removed because he knew too much and tried to blackmail both the church and the mafia, whose money he had laundered. But Michael's dealings with him were above board and he was no danger to Corleones.
In fact, once the Immobiliare deal was ratified, none of them were a danger anymore, since Michael had organized his business as a proper corporation and once it had the controlling interest, it wouldn't have greatly mattered whether Michael himself lived or died.
Calo going for Luchese in revenge for Don Tommasino and maybe Altobello's poisoning made sense, but the rest of it was just gratuitous and stupid, IMHO.
This also makes me wonder what exactly Michael gave Vincent. I mean, he intended to head the corporation himself, with help of financial managers and lawyers no? So, did he just give Vincent the illegitimate part - Zaza's leftovers?
And if so, why the whole "you can call yourself Corleone" part? Why not just have Corleone crime "family" become Mancini, clearing the Corleone name and blood family of crime associations once and for all?
Would have been much more realistic, too, given how RL mafia families changed names throughout their history when bosses changed.