Lets put it this way, if the 360 version has truly not affected the PS3 version, then everything will be ok, because it's the truth, and while rumours will still fly about they'll never have any proof to make them legit.
If it's true that the 360 version has compromised the PS3 version and they're trying to hide it, then sooner or later the truth will come out in one form or another, and at the rate things are going, it'll be 100% confirmed if true before the game is even released, and man will it bring a shit, a shit storm so big that it'll ruin S-E reputations as a competent even relevant RPG maker this generation.
So really it all falls on S-E, because at the end of the day the truth will be revealed for better or for worse.