And yes as far as I know it is not about him resigning or anything. To my knowledge, his duty period is over.
I really wonder why the BCCI says that they are not going to take back Ganguly again at this moment. Especially after he has done a really good job for Indian cricket. The only logical explanation is going to be that they have someone better than Ganguly. Will Roger Binny be more effective than Ganguly!
He most probably got kicked from his position because he wasn't willing to join BJP which ended up screwing him over. Think!
You know, politics plays a significant role in sports in India. There is obviously no doubt that Ganguly's unwillingness to join the BJP was a crucial factor that impact his re-election as BCCI President in spite of his absence from the BJP. Having said that, I think he did more than a decent job in my opinion.
However, I do agree with you that he did take a huge salary for the job he did. The amount of salary that he received seems to be a large amount considering the amount of work he did. The BCCI, on the other hand, is exactly the kind of organization that can easily afford to spend that kind of money.