I had an opportunity to review Hyatt's diary entries in Bartlett's book.
That was a different soldier who committed suicide. In the entry immediately above that one is the mention of Lt. Bonner being sick with "bilbous fever". Those entries were in August 1863. The whole unit was doing Provost Guard duty during that time period, which probably explains Lt. Bonner's detached duty.
Apparantly, Bonner survived the war. Diary mentions:
Sept. 29, 1863 - Lt. Bonner was wounded in the hip and arm at an engagement at Mrs. Sterling's Plantation.
Sept. 12, 1864 - "Spent a pleasant day at *Capt.* J.M. Bonner's place."
I would guess that after his injury, he was discharged and assigned to some sort of homeguard or non-combatant service and given a promotion to Capt.