Clarkson was to start his new job at North Melbourne from November but his role remains under a cloud as the AFL investigates the allegations, including one that Hawthorn coaches urged a player to have his partner's pregnancy aborted.
Aboriginal Australian Thomas said he had spent time one-on-one with Clarkson before the allegations surfaced last month and described him as a "great coach".
"Our relationship has been pretty good," he told Channel Seven.
"He’s a legend of a coach and I love him as a person. (I) haven’t spoken to him since (the revelations), but hopefully it goes alright."
Thomas said he would support Clarkson, who led Hawthorn to four AFL championships between 2008-15, coming back to the Kangaroos.
“Yeah, definitely," he said.
"He’s a great coach and we’d love to have him, but we’re just waiting to see what happens (with the AFL investigation). Whatever happens, happens but, yeah, would be great to have him."
Former Hawthorn head coach Clarkson and his one-time assistant Chris Fagan have denied any wrongdoing during their time at the club.
The accusations by unidentified players were included in an independent review commissioned by Hawthorn and were reported by the Australian Broadcasting Corporation.
The AFL named a four-person panel this week to investigate the allegations, looking specifically at the period from 2008 to 2016, and to report its findings before the end of the year.
The investigation has been complicated, however, by the players' refusal to disclose their identities to the AFL.
