The wedding took place at the Tokyo Institute of Technology; live human guests were in attendance, along with an MC and a priest. See Sal and Nene get hitched in the following video:
(Sal9000 marries Nene Anegasaki video)
Science fiction fans are not entirely unprepared for the sight of a real person marrying an anime character, thanks to the works of writers like William Gibson. He popularized the idea of a relationship with a virtual person in his 1996 novel Idoru, in which a virtual person, an idoru or idol-singer, seems so real to fans that some of them want to marry her.
A Remarkable Coincidence
'There is a philosophical problem of some difficulty here...' - Arthur C. Clarke, 1953.
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Rogue AI Replicated Itself
'Sapiro’s computer just kept dialing at random, hanging up on humans, until it got a fellow computer of the same type as itself.'