The Lithuania defender tore ankle ligaments in a tussle with Dundee United striker Johnny Russell last Saturday's 3-1 Tannadice defeat and is now likely to miss the remainder of the Clydesdale Bank Premier League campaign.
The 29-year-old - who is out of contract in the summer - was due to undergo surgery today and then faces a further 12-week recuperation period.
That led McGlynn to admit the defender, who joined the club in 2008, may never pull on a Maroon shirt again.
The Hearts manager said: "Has he played his last game? Possibly, yes.
"It's a blow for Marius who has had two or three years without any injury, playing every week.
"Whether he's played his last game is getting away from the fact that it's a blow for the boy right now.
"He is the captain of the football club, he picked up the Scottish Cup in May. Unfortunately he was not able to play in the League Cup final anyway through suspension, but if he was fit he would have played in all the other games and he still would have been the captain and taken us through to the end of the season.
Zaliukas' absence now leaves McGlynn with a choice to make as he seeks a new defensive partner for Andy Webster.
Darren Barr and Danny Wilson are options but the manager has already acknowledged that his squad is short on numbers.
"This is another experienced player that we have to go without," he said. "Danny Grainger has done his cruciate and Jamie Hamill is still getting over his.
"We don't have loads of experienced players. Hopefully we have used up our bad luck. We can do without any more of these long-term injuries."
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