Haidara was stretchered off with a knee injury during Sunday's Premier League game at the DW Stadium after being caught by a high challenge from McManaman, who escaped punishment from referee Mark Halsey.
But Whelan, whose own playing career was ended by a serious injury, insists there was no malice intended by McManaman.
Whelan told BBC Radio 5 live: "The ball was there. Young McManaman went in for the ball and got the ball as clean as a whistle, but in the follow through they collided.
"The referee saw it all, he had a clear view on that. He hasn't gone over the ball. That's an accident.
"There is not one ounce of malice in Callum McManaman. He is an enthusiastic young boy. He has got great prospects. He was very upset by it all."
Wigan manager Roberto Martinez also insisted after the game that there had been no intent from McManaman to harm Haidara.
"Remember it's Callum's full debut in the Premier League. I haven't seen the replay, I believe he touches the ball and then it's a bad challenge, but it's nothing malicious, he's not that sort of boy," Martinez told Sky Sports.
"It's the normal enthusiasm that you get in your debut."
Newcastle boss Alan Pardew was outraged by the challenge and felt referee Mark Halsey should have sent off McManaman.
"It is an awful challenge. The pictures speak for themselves," said Pardew. "I thought it was a bad challenge and I was 60 yards from the incident.
"The players knew because they were on top of it and there was a lot of bad feeling about that incident when it goes unpunished. He (Halsey) said 'If I've missed it I apologise' - that was at half-time."
Former Premier League referee Alan Wiley , meanwhile, has offered his support to Halsey over the incident.
"When the ball goes out towards the touchline, Mark will probably think McManaman has played the ball because he cannot see the challenge as it is," Wiley said.
"It is a one in a thousand situation where at the opportune moment, a player runs across his path and unfortunately, that (the foul) gets missed."