It can prove to be better for his future as he'll certainly try to concentrate more by playing some domestic cricket. There is no doubt that he'll be back to the national side in the future.
Another point is, if BCCI found Pathan's performance so bad to call him back from the ongoing tour, why not VRIENDRA SEHWAG? I just don't understand why are we carrying him unnecessarily who has failed to perform since quite a long.