There are three fully canon examples of an Agent leaving a 'civilian' after possessing them.
In the Animatrix segment "Detective Story", Trinity shoots a private detective who's just been taken over by an agent. No sooner has he been shot then the agent leaves (to find a less disabled host) and he is restored to his former self with no obvious ill-effects aside from the fatal gunshot wound.
In the comic "Day in...Day out" which you can read online here, a civilian is taken over by an agent. After an extensive firefight (in which 'Agent White' loses an arm) she is restored to her body and has no memory of the incident but still has the injuries suffered during the assault.
This is extremely similar to the comic "Wrong Number". An Agent takes over a telephone repair engineer and kills a redpill, then regains consciousness with no memory of having been possessed.
The last instance offers no clarity as to the mental state of someone being left by an Agent but when Trinity shoots the helicopter pilot (in the famous "dodge this" sequence), we see the pilot revert to his former self physically within seconds. The agent reappears a few minutes later, after having possessed another human.