The way I see it, Take Two saw that Bioshock Infinite was not making profits (it is speculated that it had a budget 200 million), so they gave Ken Levine and Irrational Games little choice. They were the ones intent on shutting Irrational Games down. They didn't want to lose Ken Levine and his talent, though, so they gave him a special offer, to make a smaller game with a smaller team.

It's only speculation, but it makes sense to me. Take Two was the distributor for GTAV, and that game made lots of money. Bioshock Infinite was definitely losing them a lot of money at the same time, despite the success of the game. It just had too bloated of a budget. Maybe their hope right now is that Ken Levine, with his small team, will make a low-budget runaway success game like DayZ or Minecraft (unlikely, at least on that scale, but I can understand why).

It simply does not make sense to me that a single person would lay off almost an entire team of developers just to focus on "his vision". It makes much more sense that Take Two was the one dissolving the developer, but gave Ken Levine special treatment so he can make the game he wants to make.