Tensions boiled over when fan groups displayed hostile banners directed at both men, prompting Keller to address the situation at an emergency press conference on Thursday.
“We were able to bring him (Emegha) in thanks to BlueCo two years ago; many big clubs approached us this summer," Keller said.
"Our priority is to keep our striker and leader. We found the best balance with this agreement, which allows us to keep the player, then let him leave for Chelsea in a year.
"Something happened that I couldn’t have imagined. I saw a minority of people in the West Stand attacking the institution, the project, and our captain. It’s unacceptable; these are not our values. Attacking our captain is not right. The fans support us.
“We used to communicate a lot, including in the National League. But that’s changed over the past two years; it’s sad. And what happened on Sunday no longer respects our club’s rules; we don’t accept it."