The midfielder underwent surgery last month and will miss the remainder of 2012/13.
"The rampaging Fletcher of old has gone but I'm sure he will be a success in a better-paced job," Sir Alex wrote in his Southampton matchday programme notes.
"We hope to have him back in action for next season and there will be a different role for him along the lines of how he played this season, sitting in front of the back four as the holding midfielder.
"Darren coped well during the last few months and he made a return to football [after his initial spell on the sidelines] with 10 senior appearances. His treatment was going well, but the problem surfaced again and the advice was [to] have surgery. The decision was taken with Darren's long-term health in mind just as much as getting back to his career.
"It hasn't been an easy journey for him, but he has shown great courage. There isn't a nicer boy at the club and he's a star professional. All his team-mates wish him well and I am sure the fans join me in wishing him a good recovery and a speedy return to football."