Thompson, a two-time premiership coach at Geelong, was James Hird's assistant before Hird was handed a 12-month ban by the AFL in August 2013 over Essendon's use of supplements in 2012.
Thompson has been appointed on a one-year deal as senior coach for the 2014 season.
Hird is contracted for 2015 and 2016 and the Bombers have locked in the club great to resume as senior coach next season.
Thompson, who like Hird is a premiership captain at Essendon, is considering his options and could be the subject of coaching offers from rival clubs at the end of 2014.
Goddard told Seven's AFL Game Day on Sunday the players were right behind Hird's return next season.
The reigning best and fairest added he wanted to see Thompson remain in Essendon's coaching department in 2015.
"We definitely are (welcoming Hird's 2015 return)," Goddard said.
"In an ideal world if those two can work together like they have in the past … it would be a pretty good combination."
Goddard said Thompson was more than capable of handling the adjustment of going from senior coach back to being an assistant.
"He has in the past so there's no reason why he can't again," he said.
However Thompson has spoken previously about the burn-out factor in coaching.
Doubts remain over whether the 50-year-old wants to stay involved in coaching beyond 2014.
"I guess that's a decision he has to make and what he actually wants to do," Goddard said.
"Whether it's to stay in footy or get away from it."
