Although not a confirmation per se, a good sign has been raised over at Siliconera, which posted an article talking about the new structure at Atlus. Here is a quote regarding how Sega is handling Atlus:
"Sega Sammy Chief Operating Officer Naoya Tsurumi is now the president of Index Corporation and Yasuhiko Hamada is the Executive Vice President.
Yukimasa Murakami, the Managing Director of Index Corporation before the acquisition, is still the managing director of the new Index Corporation.
Yakuza creator Toshirio Nagoshi, Sega game director Yukio Sugino, and Atlus USA president Naoto Hiraoka are on the company’s board."An interesting thing to note is the addition of Toshirio Nagoshi, creator of Yakuza and Monkey Ball, and Yukio Sugino, executive supervisor of such games as Space Channel 5: Part 2, Sonic Adventure 2 Battle, and Guardian Heroes, to the company's board.
Overall, Sega seems to want to keep things the way they were before. In fact, the buyout was carried out under a subsidiary called Sega Dream Corporation. As of now, that name has been changed from Sega Dream Corporation to Index Corporation. This just further proves how dedicated Sega Sammy is to keep Atlus functioning as it was before.
For now, I would say things are looking good. Still, if you feel different, please let us know in the comments below!
Read more at http://www.siliconera.com/2013/10/31/whos-charge-index-corporation-atlus-parent-company-now-sega-owns/#WXJCcRTdRELbOoqS.99