The German World Cup winner made a reported £20m move to Los Blancos after refusing to extend a contract with Bayern which expired in 2015.
Hopfner has admitted that the Bundesliga champions could not afford to let Kroos leave for free at the end of next season, and therefore came to the "right solution" when deciding to cash in on him.
He told Kicker: "In the case of Kroos, the board of the club has taken the best decision.
"After it had been impossible to sign an extension during the phase of negotiations, the board had to consider the intrinsic value.
"Toni Kroos did not want to sign a new deal, therefore he would have been a Bosman player in 2015. Because of this, a departure has been the right solution."
Bayern replaced Kroos with Madrid's decorated Spanish international playmaker Xabi Alonso.