Sega basically has me confused. They seemed like they were trying to pare down their operations and focus on PC in the game space and far fewer franchises - i.e. only bigger sellers like Sonic, Football Manager and Total War.
And then they go and buy Index.
As for Konami, it really is sad. I wonder what would happen if Kojima left them.
I think it makes more sense if you consider Sega's press release for their old distribution agreement.
http://indexweb.jp/news/2012/news_20120217_01.html
Index Holdings announced today that starting from April 2012, they have entered into a distribution contract with Sega with regards to the retail distribution of games under the Atlus brand. There are no further details at the moment, but it seems that Sega will be helping Index distribute games released under the Atlus label in Japan in the retail market.
Edit: The last two lines of the press release states that by this agreement, Atlus hopes to leverage on Sega's larger domestic retail distribution network in Japan, while Sega plans to announce details of a diverse offering of various products leveraging on Atlus' strong IPs. This sounds like a sort of partnership that could indicate that Index Holdings is too small for Atlus' growing ambitions. Or... they're running out of money.
Basically I feel they view Atlus the same way they do Sonic or Miku, where they're not just games, but brands that they can make a huge variety of heavily targeted products for.
Now, obviously Sega doesn't own Miku, but with Sonic especially they make kids shows, comic books, and all sorts of merchandizing for the lucrative kids market. Miku is more the otaku (nerdy Japanese teens-to-young-adults, also lucrative), and I'm assuming they want to use Atlus' brands to target the otaku audience in the same way.