Rangers boss Stuart McCall says he feels sorry for Gael Bigirimana, but admits he should never have been signed.
Chris Gunter will stay at Reading, after the club took up the option to extend his deal by another year.
The highly-rated Spaniard's potential has again been underlined by Latics' run to the semi-finals of this season's FA Cup.
There has been speculation over Martinez's future for each of the past two summers - with Aston Villa and Liverpool heavily linked with his services - following his success in steering Wigan clear of relegation from the Barclays Premier League.
Whelan has said previously that former Wigan player Martinez, 39, will eventually leave the club with his blessing but he wants him to stay as long as possible.
Whelan told BBC Radio Five Live's Sportsweek programme: "We have known each other and been together a long time. Hopefully that will continue.
"I will lose him, I don't think there is any question about that.
"He is a top-class manager and he will get one of the top clubs in Europe.
"The big clubs in Europe, when they want a manager, Roberto is obviously the man. He is stone-cold brilliant as a manager."
There was a downside to Wigan's superb 3-0 quarter-final win over Everton in that Premier League action elsewhere meant they slipped back into the bottom three.
But Martinez has been involved in a relegation battle every season since he took charge at the DW Stadium in 2009 and his last two escapes have been particularly remarkable.
Whelan is confident he will achieve safety again.
He said: "We have been there before and fought our way out of it.
"We are going to do exactly the same again, I hope.
"We have played well all season and just had so many injuries and bad luck.
"We played Everton off the park and have done that so many times this season but at times we have had up to eight players injured.
"It is very difficult to take that kind of punishment."