The FA is allowed to take retrospective action for "exceptional" incidents - and Scudamore said the challenge should have been judged as just that. The FA announced this week 21-year-old McManaman would not face action as one of the match officials had seen the incident, even if not the full extent of it.
Scudamore said: "I don't think anybody in the Premier League, perhaps bar Wigan, would have complained had they decided this was exceptional. That's where the Premier League is on this, I don't think the rules need changing, I don't think the line needs moving. If they have the ability to deal with an exceptional incident, it looked to most of us that was an exceptional incident."
He added: "What we don't want is re-refereeing, everyone is agreed on that. I think the current system works and no one would have criticised the FA if they had decided that was exceptional."
The FA's rules limit retrospective action to off-the-ball incidents unseen by match officials unless they are exceptional circumstances and the governing body said this had been agreed with the leagues, the PFA and referees.
Scudamore insisted that no change to the rule was necessary but that the FA should have accepted that the McManaman tackle should be dealt with.
Speaking at the launch of 'Creating Chances' - the Premier League's annual report of its work in communities, he added: "I can understand why given what's happened this week the FA are looking for some cover and I don't blame for that.
"Yes there is a system that says there are some very clear guidelines that says under what circumstances they can effectively apply retrospective disciplinary action and like all guidelines and rules there is in their view a fixed line.
"But we live in a nuanced world, nothing is that precise, and my view is that currently they have the ability in exceptional circumstances to take retrospective action."
Haidara suffered knee ligament damage after the challenge by McManaman, but no action was taken against the Wigan player during the match.