Flanagan was on Tuesday hit hard following the NRL's findings into the Sharks' controversial supplements program in 2011.
The popular coach was given a 12-month ban, which could be reduced by three months if he completes certain educational tasks, leaving the Sharks without a head coach for the 2014 season.
The club have said they will support Flanagan, who has until January 15 to appeal the decision.
It is the second time in 12 months that Flanagan has been stood down over the supplement saga which has engulfed his club and the NRL.
Assistant coach Peter Sharp took the reins in March for two rounds while Flanagan was stood down on the recommendations of an independent internal report conducted by Tricia Kavanagh.
Sharp could again be considered by the Sharks should they be seeking another quick fix.
But if a more permanent solution is desired, Kimmorley has emerged as the frontrunner.
The 37-year-old has ambitions to become a head coach and strong ties to both the Sharks, where he played between 2002 and 2008, and Sharp, who coached him at the Northern Eagles in 2001.
Kimmorley has done his apprenticeship as an assistant under Canterbury's Des Hasler and is currently an assistant coach at Canberra under Ricky Stuart.
But the pair have a strained history dating back to Stuart's time as coach at the Sharks when he chose not to re-sign Kimmorley.
Stuart also coached Kimmorley for NSW in 2005 when the halfback threw an infamous intercept to Matt Bowen to lose game one of the series.
"I learned then (in 2005) that Kimmorley was not a big-match player," Stuart wrote in a newspaper column in 2009.
"And I knew that when I later moved to Cronulla. We tried our best to work together, but it didn't work.
"That's why my board clapped the night I told them I had released Kimmorley."
A formal release has not yet been requested, but the Raiders are unlikely to stand in Kimmorley's way if he was to secure a head coaching role elsewhere.
Former Wests Tigers and current Kangaroos coach Tim Sheens has also been suggested, although he is considered a longer shot due to his rocky relationship with several former Tigers players on the Sharks' roster.
It is understood the Sharks have discussed pairing Kimmorley with Sharp, who would take on an overseeing role.