The retired Germany international, who moved to Old Trafford from the Bavarians at the beginning of last season, is already on his way out following the arrival of Jose Mourinho at the club.
Rummenigge has been stunned by reports that the 32-year-old World Cup winner has been excluded from United's plans and told to train with the reserves, and says it will make other players doubt the club's credibility.
"When I read that I could hardly believe it," Rummenigge told Bild.
"One or two players are going to think long and hard in future about whether they want to go to such a club.
"Nothing like that has ever happened at Bayern Munich and it will never happen."
Schweinsteiger made just 18 Premier League appearances at the Red Devils last season as he struggles through form and injury, under Louis Van Gaal.