I don't think NFL is concerned anything about any player or coach's career here, they care about profits and ratings, and issues such as this one brings them all to the table. It keeps the national tv viewers engaged in hating the successful, the 4 game suspension is also very timely since Brady will come back and play against the colts.
Now the funny thing is, what if Jimmy G comes in and play really well? Or Brady's career in New England ends just like how it started? What if, god forbid, the pats trade him mid season for a first round pick next year to make up the pick that we will lose? Those are unlikely but not without a question can happen this season.
But I think Brady will appeal and reduce it down to 2 games. The pick and money are gone nonetheless, this is the NFL's way of bringing us down to the level of competition, it must suck really bad for the competitiveness of the players and coaches, but to the NFL as a whole, a more equal competition field means longer life and better viewer engagement. It's all part of the business and that's why Kraft is supporting whatever Goodell is doing. Hey look, it's the NFL offseason, with the NHL and NBA playoffs all going on, yet most people are still following the NFL at this time due to this deflatgate stuff, this to me is a winning on Goodell's books. Remember he is a business man first, and unfortunately for us pats fans, we are just being used as a means to an end.