This is a much more feesable explination. E you yourself know from your buisness ventures a team must click. Kelly is new and he has to show that he is that dude running that team. It makes a statement and a shows a new regime is in and the bullshit wont be tolerated no matter how good you are, or how good you think you are. The fact the eagles are going to have to eat 6 million over this shows they are ready to move forward with Chip and the Reid era is truly over.
This is what I think it is. It's just dirty they are killing his character in the process. But that is how Kelly is covering his ass. Management, media, and the fans will give him a pass because he's "Cleaning up the team". It's really a no-lose situation (beyond the massive lose of talent). It blows up on his if his offense stagnates though...but he's banking on being able to just plug someone else in.
It's draconian. Essentially Jackson is being used as the example. He is being sacrificed in order for Kelly to impliment his master plan. His teammates loved him and he was never really a "real" problem so cutting his was apparently (from what we all know) a very harsh decision.
Like you said. Kelly is saying that the Reid era is officially over.