Indeed, it was the first time Madoka had a FULL picture of the system, and used it damn well.
As to being so mean as to leave Homura again... She didn't have a choice. What she did to the world and herself through her wish was not a cop-out, but the only possible way of solving the problem on the local and general scales. And her current status, godlike as it may look, is in reality far from beneficial. But she accepted it, for the sake of being able to do what she wants to do.
Seriously, though, it looks like Kyuubey's miscalculation in more ways than one. Did he ever consider the possibility of Gretchen destroying the whole universe? That would devalue any amount of energy she could produce, and wipe out all the civilizations including Incubators. Nice job, Kyuubey, be thankful that Madoka managed to save your butt among other things.
