Did pilots with the rank of General actually fly bombing missions over Germany as depicted in "Twelve O'clock High?
They did, yes. The character of Brigadier General Frank Savage in the film was inspired, at least in part, by Frank A. Armstrong who took over two underperforming Bomb Groups (the 97th in July 1942 and the 306th in January 1943) and flew combat missions with both. Though a Colonel when he took command of the two groups, he continued to fly in combat after promotion to Brigadier General in February 1943.
Other examples include Brigadier General Ira Eaker, who flew on the first USAAF B-17 raid in 1942; Brigadier General Haywood Hansell, who preceded Armstrong as commander of the 1st Bombardment Wing; and Brigadier General Robert Williams, who led the Schweinfurt raid of August 1943 that suffered extremely heavy casualties.