So long as they go the route they did with Relic entertainment and let Atlus do their own thing, it should be just fine. Depends entirely on if they do that or not though.

I don't' think we'll see the death of Atlus USA if only because they are arguably one of the strongest localization groups we have right now, and I don't think even Sega is silly enough to not put that to use, not after how much they paid for it.