Menton said that the Republic of Ireland's impressive performance at the World Cup finals showed the squad could prosper without the former captain.
"This team will go on without him," Menton, general secretary of the Football Association of Ireland (FAI) told the Daily Mail newspaper.
"There is a limited life cycle to a player's career and it had to come at some stage. It happened to be sooner than expected but so be it."
The Republic reached the second round of the World Cup before going out to Spain on penalties.
Keane, 30, and Ireland's most influential player, was sent home in the week before the World Cup finals after a blazing row with manager Mick McCarthy after a training session.
The future for Irish football is very good
The Manchester United midfielder, who said he would never play for Ireland again under McCarthy, was given the chance to return to the squad but refused to apologise for his outburst.
On Monday, the FAI announced that McCarthy would be staying on as manager for a further two years.
Menton said he was confident that McCarthy and the Irish football authorities would be exonerated by an independent inquiry into the way the World Cup campaign was handled.
"The Roy Keane issue has gone away," added Menton.
"I think the team and their performances showed why it has.
"It would be very difficult for anyone to argue that the team would have done any better with him here."
Menton said the Republic's performance at the finals showed the team had every reason to be confident about the future.
McCarthy's side were knocked out by Spain in the second round on Sunday, losing on penalties following a 1-1 draw after extra time.
They progressed from the group stages after draws with Cameroon and Germany and a win over Saudi Arabia.
"The future for Irish football is very good," Menton said.
"I keep thinking back to the game against Holland two years ago in September when seven of the 11 were 25 or under.
"There is plenty to come from this team in the 2004 European finals in Portugal and the next World Cup in Germany."
Menton was talking to reporters in Seoul on the eve of the squad's departure for Dublin.
Around 100,000 fans are expected to greet the squad at Phoenix Park in the Irish capital later on Tuesday.