Thomas, a key member of the Magpies' 2010 premiership side coached by Malthouse, will become a restricted free agent at season's end.
At a press conference at Melbourne Airport on Friday morning before the Blues clash with Brisbane Lions at the Gabba, the Carlton coach interrupted a reporter's question about Thomas.
"I'm not talking about Dale Thomas. I just wish him the best for his surgery," Malthouse said.
"If you're going to say something about free agency, free agency is open to every football club."
Thomas, 25, will miss at least the next 12 weeks after undergoing ankle surgery.
The coach and midfielder share a close relationship, and would routinely seek out each other pre-match for kick-to-kick sessions.
It wasn't long ago that Carlton's clash with the Lions would have been eyed as a glorified kick-to-kick session for the improving Blues. But that all changed when the Lions upset Essendon at Etihad Stadium last week.
Malthouse rates the Lions as "a good side" that benefits from the availability and leadership of veterans Jonathan Brown and Simon Black.
"To beat Essendon at home is an enormous task … and they play their home ground very well, so we've got a massive job in front of us," he said.
Two months ago, the Lions belted Carlton by 40 points in the NAB Cup Grand Final. Malthouse refused to label that result irrelevant to this contest.
"You can't dismiss it; you can't just be flippant about it. It was a very, very good victory by a side that we play tomorrow," he said.
The Lions were aggressive from the outset against the Bombers, and Malthouse expects a similar greeting on Saturday night.
"I don't have any other opinion of Michael Voss other than that his side play desperately hard football for him. It's the way he played. Teams end up emulating their coach, and our boys would expect nothing different," he said.
Malthouse believes his side conceded "too many soft goals" in its 18-point win over Port Adelaide last week, but hopes to "close up" the Lions' scoring options.
Even so, the Blues' defence appears to be developing into a more cohesive unit. Malthouse admitted that the backline he selected in February practice matches had "changed considerably", and his defenders were still adjusting to each other.
"Those things do take time," he said. "(Simon) White didn't play a lot of football last year but he's played five or six straight. (Michael) Jamison and (Lachie) Henderson were in and out of the side last year, hopefully they can stay together. And we've added a couple of other players from various positions on the ground, just to see how they jell.
"The test now is whether that stands up against sides going forward."
