Now Green hopes Ponga's departure helps secure a new Thurston deal for the Cowboys.
Thurston, fellow co-captain Scott and Dally M Medallist Taumalolo are among more than a dozen big-name Cowboys off contract next season.
"We expect Kalyn to go there. We are disappointed but we will move on," Green said of Ponga's Newcastle deal.
"It probably takes a bit of pressure off trying to keep some of the other big names like Johnathan Thurston, Matt Scott and Jason Taumalolo.
"We are disappointed to lose him but we have got the big picture in mind, we have a plan in place."
The Knights had hoped Ponga would don the Knights No.1 jersey next year.
Green was "not too sure" if Ponga had asked for an early release but he made it clear the teenager was still needed until his Cowboys contract expired at the end of 2017.
"Kalyn's contracted to us for next year, he's part of our plans for next year and as such he's expected to play for us," Green said.
"So I'm going to pick the best team possible and if Kalyn's part of that then he'll be in the team, simple as that."
North Queensland had hoped to offer Ponga a three-year extension but Green said they could not compete with the cashed-up Knights deal.
"There were obviously things that were important to Kalyn in weighing up his decision - things that we probably couldn't match," Green said of Ponga's lucrative Newcastle contract.
"Newcastle are paying what they felt they were able to pay.
"If it came down to money we were probably never going to be in the hunt if that's what was the most important thing, and I'm not saying it is, but clearly that's made up part of his decision."
Ponga made his NRL debut on the wing in the Cowboys' finals win over Brisbane in September as an injury replacement.
He played in the preliminary final loss to Melbourne a week later. It's not the first time Ponga has been in demand.
As a junior he was chased by six clubs and four sports before committing to the Cowboys.
