Ganguly, who captained KKR in the inaugural and 2009 season, was completely ignored in two rounds of players` auction for the fourth edition starting April 8.
The snub to the flamboyant batsman triggered angry protests in Kolkata. Khan pleaded with the fans to understand the compulsions behind the decision.
"It`s with very heavy heart that such decisions are taken. I don`t do cricketing decisions anymore because in the first year when I did it, I have not done very well," Khan said.
"I feel very sad for my team, for the city that my team represents. I feel very sad for the state. I feel very bad for my children. So all the decisions are now taken by the cricketing brains. The main aim is to perform well since in the last three years we have performed badly and I am sure that Dada also wishes that we do well," he added.
Khan said the team, which has bought Gautam Gambhir for mind boggling Rs 11 crore, cannot be about one individual.
"Dada is like my younger brother. The team does not consist of one or two people. It is a team of 20. We used to feel very bad about our loss. We have even cried when we didn`t win in India as well as in South Africa.
"We only want to win the championship for Kolkata. We all want to do that including Dada. We have to put sadness, issues and thoughts behind sometimes to achieve a goal. We all have to make some sacrifices we understand that," he told `Times Now`.
Khan said the controversies should now end and KKR should be allowed to function smoothly.
"In season one, we had a lot of controversies and in the third IPL season, we had so many problems so my message to everyone is to give me a chance to run KKR without controversies. Let me play the game with the spirit of the game," he said.