My flight commander, when I was a student at RAAF AFTS, was a Sqn Ldr who was afflicted with severe stutter. He flew Canberra's, exchange RAF V bombers (including cloud penetration of the Maralinga nuclear tests), was a flight commander at RAAF CFS, CO of the first F4 squadron. Retired as an AVM and spent a number of years working in industry and government after the RAAF.
Stutter didn't seem to restrict his career.
I would give your friend some air time, keeping him occupied with "flying duties" and see how he copes.