I don't get why people are freaking out. Atlus itself is a publisher, just as Sega is a publisher. This buyout doesn't necessarily mean that atlus games are going to be published by Sega (aka, not brought over here due to lack of interest).
As long as Atlus keeps up their ability to publish and localize games, I don't see this being an issue. Should hopefully be as if nothing ever changed, if not even better.
Why would Sega want to pay upkeep for two separate publishing entities? That seems redundant from a business point of view.
Remember. This is NOT Sega Corporation, but Sega Sammy the holdings company.
It will certainly not affect day to day operations in regards to localization, at least not right away.
However there is mentioning of a restructuring, so who knows... I have all the reason to believe the restructuring is to deal with the sections of Index that are bleeding money. (I.E. Not Atlus.)