Michael Berrios was stabbed to death in December 2004 on a Queens street, police said.
A statue of St. Jude and plaques with deceased parishioners' names were removed, sparking confusion.
Thursday was the deadline for the school to submit a proposal to raise money to keep its doors open.
The 27 "at-risk" schools have until Jan. 3 to prove they can survive without subsidies or face closure.
With attendance declining and funds dwindling, several Catholic elementary schools will likely close.
Parents and alumni of St. Jude School say school officials aren't helping them save the school.
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