Togo were due to face Ghana in their opening Group B match in the African Nations Cup tomorrow in Cabinda, but it is still uncertain whether the Togo team will return home.
O'Neill, however, believes Salifou will be badly affected by the incident.
The Northern Irishman, interviewed on BBC Radio Five Live's Sportsweek programme, said: "Something like that is going to live with him for a very long time, if not for the rest of his life. It was very, very harrowing and he is actually a very sensitive lad.
"He's very popular in the dressing room. He's very quiet. He's got a wry sense of humour, but he's an exceptional fellow and I think he will take this very badly indeed.
"We have a number of people at the football club who I think can help him. Some of the players who are quite close to him will give him as much counselling as possible but I'm hoping in time he will be able to settle down and get back to playing."
It was confirmed on Friday night that the bus driver was killed in the incident, while an assistant coach and a press officer are also reported to have died from their injuries.
O'Neill added that he would prefer the players to come home if that is what the national federation decided.
Salifou spoke on the official Villa website yesterday, describing the team's ordeal and underlining his personal desire to leave Angola.
He said: "We all want to go home to Togo. We don't want to compete in the tournament because our assistant manager has been killed and also the press and communications officer. As a team, we have made this decision.
"We must wait, however, so that we can speak to our federation president and some people from CAF and let them know that we don't want to play. We can't play in these circumstances and we want to leave for home today.
"To be honest, I can't sum up how I feel at this moment. My parents keep calling me from Togo every 30 minutes just to make sure I am okay and to see how things are going here."