The Manchester United superstar – who has netted 53 times for his country in 119 appearances – has not been selected by manager Gareth Southgate for the crunch Group F World Cup qualifier at Hampden Park on Saturday.
And former Motherwell manager McGhee said: “I don’t think it’s a bad thing for us that Wayne will not be there.
“He knows what it is like to play against Scotland.
“I would be surprised if this was the end of his England career.
“I’m a massive fan of Rooney. He has been an outstanding player for Everton, Man. United and England but the world changes.
“Harry Kane is the top scorer in the English Premier League now and he and other players have come in and are doing well.”
Scotland go into this Saturday’s Mount Florida showdown, which kicks off at 5pm, down in fourth in Group F six points behind England but just two points behind second placed Slovakia with five games remaining.
And McGhee doesn’t think this match is ‘must win’ for the Dark Blues’ hopes of qualifying for a major tournament since the 1998 World Cup in France.
“Whatever happens against England we have to win the other four games anyway,” added the 60-year-old. “Depending on what happens in the other fixtures, then win, lose or draw it could still leave us with a chance of making second spot.
“However I think we have got to assume the worst and imagine we have to win the England game.
“If we go into the match with the attitude that it is a must win game then there will be no surprises in terms of what happens elsewhere.”
If the Scots are to produce a famous win, then key men will surely be Celtic stars Craig Gordon, Kieran Tierney, Scott Brown, Stuart Armstrong, James Forrest and Leigh Griffiths, part of the Hoops side which romped to a domestic treble this season under Brendan Rodgers.
“Hopefully that will be an advantage for us,” McGhee said.
McGhee added: “I think the Slovenia game (a World Cup qualifier in March which Scotland won 1-0 thanks to a Chris Martin goal) showed the Celtic players’ value to the team.
“Hopefully it is an advantage to us having a group that is so familiar to each other and playing with such self confidence.
“We can immediately implement tactics involving these players which would take longer if they weren’t team-mates at club level.
“They have that understanding of each others’ games that has been brought about by Brendan and we can only benefit from that.”
As a Scotland player way back in 1984, McGhee headed home a cross from current Scotland manager Gordon Strachan for our goal in a 1-1 Home International draw against England at Hampden.
That game 33 years ago was played in front of over 73,000 fans at the old terraced Hampden. Scottish football pundits have criticised the modern 52,000 all seater Hampden for lacking atmosphere and making it an easier place to come for opposition sides.
McGhee said: “I think it is up to our players to intimidate the English, not the crowd.
“The players need to give the crowd something to back.
“We have to start the game positively and give the crowd the feeling that we can win.
“That way the crowd are on their feet, motivating and inspiring the Scottish rather than intimidating the English.
“It’s not as if people like Harry Kane don’t know what it’s like to play in intimidating atmospheres anyway. They have played in European Championship finals and at places like Old Trafford and Stamford Bridge.”
Mark McGhee was speaking at the McDonald’s and Scottish FA Community Football Day in Strathaven, encouraging youngsters to play football at a grassroots level and celebrating Quality Marks in the area.
For more information visit www.mcdonalds.co.uk/betterplay