It's pretty clear that at this point neither side wants (or in ND's case should want) to be in this relationship.
It saves both sides quite a bit of face if Kelly gets an NFL job. Hell, ND might even get some cash out of it from an NFL team. ND is a much more attractive job at this current juncture with it's current head coach (despite a mediocre record) obtaining an NFL job than firing Kelly next year after going 7-5 again. Not to mention it's pretty unusual for a college coach to get fired for looking at NFL jobs. Chip Kelly did it twice and Oregon certainly wasn't thinking of jettisoning him.
That being said, I would have no problem if Kelly was fired for his performance in the second half of 2014. I just don't think it should be because he (or his agent) are pursuing an NFL escape route that would benefit both sides.