Is Joe Paterno the only active coach to have coached against Bear Bryant?

At the end of the 2009 season, no.

Howard Schnellenberger, currently head coach at Florida Atlantic University, was head coach of the University of Miami between 1979-1982. Miami lost to Alabama, 30-0, on October 17, 1979. Schnellenberger was the offensive coordinator at Alabama between 1961-1965 under Bryant.