Froome will have his sights set on a record-equalling fifth Tour de France victory next July having had his domination ended by team-mate and fellow Britain Thomas this year.
Thomas burst out of Froome's shadow to claim a superb first Grand Tour title and the 32-year-old Welshman is unlikely to be keen on returning to a supporting role.
Although Kelly believes Sky still have faith in Froome to deliver at the end of three weeks in France, he thinks Thomas's rise will test Brailsford's man-management skills.
There are suggestions Thomas could be handed the leadership role at the Giro d'Italia, won in spectacular style by Froome this year, with the 33-year-old Froome given the lead role at the Tour.
"Will they try to get G to win the Giro and see what happens in the Tour and then let Froome really put everything into the Tour?," Kelly, a four-times Tour points jersey winner and now Eurosport's voice of cycling, told Reuters at the Rouleur Classic show in London.
"That's something I think they would like to do but would the riders be happy with that? It's going to be difficult for Sky to make everyone happy."
Thomas signed a new contract with Team Sky recently even though a move elsewhere would have earned him the number one status he has craved.
In his new book "The Tour According to G" he describes how, following an electrical fault in the hotel after stage nine this year only Froome was given access to air-conditioning despite Thomas leading his team-mate by a minute.
The relationship between Thomas and Froome remained harmonious last year, but Kelly says having two high-profile "leaders" can be hard to manage.
"Brailsford is the man with the decision," Kelly said. "If he has to go to Thomas and say 'we want you to win the Giro' is he going to be happy with that? It could get complicated.
"G might say 'hey I won the Tour this year so why can't I go back and try and win it again?'
"You can have co-leaders. But sometimes when it's in the heat of the moment and you are in the proper climbs in the race and the adrenaline is flowing things can go wrong.
"They can start fighting each other and the other members of the team can feel that. If there's rivalry between riders, the helpers in the team might be closer to one more than the other and then it can create divides."
While Froome has another chance to equal the five Tour wins of Miguel Indurain, Bernard Hinault, Eddy Merckx and Jacques Anquetil, another Briton, Mark Cavendish is also chasing down Merckx's stage win record of 34.
Cavendish, plagued with injuries and illness this year, has not a won a stage since 2016 and needs four to match Merckx.
Kelly believes Cavendish, who rides for the Dimension Data team, can return to winning ways next year.
"I think he is capable of getting the record," Kelly, who won the Paris-Nice classic seven times, said.
"This year will be very important. If he doesn't win this year, you start to doubt yourself. If he wins some big sprints next year then that could set him up for the next year too. If not it will be difficult to get back."