I don't understand why the NCAA would allow a network like this to use one of the NCAA's bowl games as leverage for their own gain. Seems kinda like putting the cart before the horse.
Dead simple. The bowls on the NFL network aren't premium properties, they're of only regional interest and therefore aren't worth a ton of cash to the major networks. But to an up-and-coming sports network looking for leverage to exert on cable networks that don't yet carry their programming they represent a nice opportunity.
Consider what has happened since the teams were announced: cable consumers in a couple of regionsl of the country (one heavily populated) have been doing the NFL Network's legwork by demanding that their local cable companies carry the NFL network. I'm sure Rutgers and KSU fans aren't alone in those efforts. The NCAA and the bowls get a bigger paycheck from the NFL network than anyone else was willing to offer, the bowls probably sell a few extra tickets to fans that would have stayed home to watch if the game were available on television in their area, and the NFL network gets a big stick with which to beat on the cable systems that don't currently carry their programming. It's a win/win/win situation for the NCAA, the bowls, and the NFL Network.
The only people who lose in this equation are the fans who want to sit at home and watch the games for free rather than travelling to see the game in person. And in the end the fans aren't really what matters, the almighty dollar is. Nicely played by the NFL Network.