The out-of-contract Lithuanian underwent surgery on Thursday after tearing ligaments in the joint during last weekend's 3-1 defeat to Dundee United.
He now faces 12 weeks on the sidelines and, with his deal expiring at the end of May, McGlynn believes the Scottish Cup-winning captain may "possibly" have played his last game for the club.
Scotland internationals Darren Barr and Danny Wilson are primed to step in and fill the gap left by the 29-year-old. However, the Tynecastle manager has already thrown prospects such as Fraser Mullen, Callum Tapping and Jamie Holt into his side and has now urged their fellow young pretenders to show they are good enough to replace Zaliukas.
He said: "We're trying to be positive and think of it as one door closing and other one opening. I look at other clubs, and there are always others worse off. Aberdeen went through a horrendous spell there with injuries. But we still have a fairly strong squad.
"We have someone like Darren Barr who can come in there, or we can re-shuffle Danny Wilson around the pitch and play Kevin McHattie. And there are others in the Under-20s who could maybe come in and do a job. You have to look at the positives and keep at it."
Meanwhile, the Gorgie boss' preparations for Saturday's Tynecastle meeting with Kilmarnock were disturbed by revelations that club owner Vladimir Romanov's Lithuanian Bank had gone into administration.
Kaunas-based Ukio Bankas has been forced to suspend activities after its share price fell to an eight-year low amid allegations it was taking too many risks.
Although UBIG, the Romanov company that controls Hearts, and the bank are separate entities the news did spark fresh concern among fans so soon after the club faced a winding-up order over a £450,000 unpaid tax bill just late last year.
Tynecastle director Sergejus Fedotovas released a statement downplaying those fears, insisting that "events in Lithuania will have very little affect on our day-to-day business".
