First, why I don't believe they meant J'onn: In S01E17 (Manhunter), Colonel Harper approves his transfer to Project Cadmus, and en route J'onn is freed by Kara and Lucy. As far as we know, Non never knew that J'onn was imprisoned, and even if he did, Non would be able to tell from asking Lucy or checking the prisoner's list that J'onn isn't there anymore.
From S01E19 (Myriad):
Non: All but the White Martian. For everyone's sake, leave that one be.
From S01E11 (Strange Visitor from Another Planet):
J'onn: That creature and its kind slaughtered the Green Martians.
The White Martians came from beneath the planet's surface, bringing fire from the planet's guts.
And they burned us all.
J'onn: It wasn't just my planet.
We fought back.
We'd known war.
But not like this.
White Martians had been toiling underground, building weapons of death.
Their technology overwhelmed us.
There was no honor in how they fought.
They herded us into camps.
White Martians are characterised as a warlike species so fierce they can enslave an entire planet of Green Martians, who are shown to be on the same level of strength as Kryptonians. When Non says "For everyone's sake", he means that even the Kryptonians would have trouble controlling the White Martian. A species as aggressive as the White Martians would ravage the entire planet and wreak havoc on Non's plans for Myriad.
From the comics' continuity, the original Martians were so powerful that
the Guardians of the Universe, fearing the ruthlessly and violently powerful Martians, genetically split the Martian race into two distinct species, white and green, preventing the asexual reproduction. They also gave these two new races an instinctive fear of fire to prevent either group from ever accessing their full potential... While the Green Martians were peaceful philosophers, the White Martians were savage warriors (Source).
If even the Guardians of the Universe fear a species, the Kryptonians would stand no chance of defeating it.