I think he was run from SMU more so because he wouldn't allow certain boosters to have access to the program. Like the ones who would eventually get the death penalty levied on the program.
His own administration also wanted him to bend certain rules in regards to recruiting and he wouldn't do it. But recruiting African American players likely had nothing to do with it. By the time he was fired following the 1972 season virtually all SWC (and SEC) schools had broken the color barrier. I think Jerry was simply falling on a grenade for his coach. Running Hayden for being a trailblazer in African American recruiting, even in 1972, seems like a little too harsh of an explanation. Then again a degree of mystery could remain. In a Sports Illustrated article covering the 1985 Iowa vs Michigan game Hayden was quoted as saying he was never given a specific reason for his firing.