Hector is indeed threatening his own men. These lines are a translation of Iliad XV.343–351.
ὄφρ᾽ οἳ τοὺς ἐνάριζον ἀπ᾽ ἔντεα, τόφρα δ᾽ Ἀχαιοὶ
τάφρῳ καὶ σκολόπεσσιν ἐνιπλήξαντες ὀρυκτῇ
ἔνθα καὶ ἔνθα φέβοντο, δύοντο δὲ τεῖχος ἀνάγκῃ.
Ἕκτωρ δὲ Τρώεσσιν ἐκέκλετο μακρὸν ἀΰσας
‘νηυσὶν ἐπισσεύεσθαι, ἐᾶν δ᾽ ἔναρα βροτόεντα:
ὃν δ᾽ ἂν ἐγὼν ἀπάνευθε νεῶν ἑτέρωθι νοήσω,
αὐτοῦ οἱ θάνατον μητίσομαι, οὐδέ νυ τόν γε
γνωτοί τε γνωταί τε πυρὸς λελάχωσι θανόντα,
ἀλλὰ κύνες ἐρύουσι πρὸ ἄστεος ἡμετέροιο.
Here are a couple of other translations.
While these stood spoiling of the slain, the Greeks found time to get
Beyond the dike and th’undik’d pales; all scapes they gladly gain’d,
Till all had pass’d the utmost wall; Necessity so reign’d.
Then Hector cried out: “Take no spoil, but rush on to the fleet;
From whose assault, for spoil or flight, if any man I meet,
He meets his death; nor in the fire of holy funeral
His brother’s or his sister’s hands shall cast within our wall
His loathéd body; but, without, the throats of dogs shall grave
His manless limbs.”
George Chapman (1616). The Iliads of Homer, volume II, p. 57. London: Charles Knight (1843).
While they were spoiling these heroes of their armour, the Achaeans were flying pell-mell to the trench and the set stakes, and were forced back within their wall. Hector then cried out to the Trojans, “Forward to the ships, and let the spoils be. If I see any man keeping back on the other
side the wall away from the ships I will have him killed: his kinsmen and kinswomen shall not give him his dues of fire, but dogs shall tear him in pieces in front of our city.”
Samuel Butler (1898). The Iliad of Homer, pp. 246–247. London: Longmans.
While the Trojans tore the war-gear off the bodies
Argives clambered back in a tangled mass, scrambling back
through the sharp stakes and deep pit of the trench.
fleeing left and right, forced inside the rampart.
So Hector commanded his Trojans, sounding out,
“Now storm the ships! Drop those bloody spoils!
Any straggler I catch, hanging back from the fleet,
Right here on the spot I’ll put that man to death.
No kin, no woman commit his corpse to the flames—
the dogs will tear his flesh before our walls!”
Robert Fagles (1990). The Iliad, p. 399. Penguin.
In the original, Hector is not accusing the Trojans of running away, but only of stopping to plunder the slain. He says that if they run away, or fail to press forward with utmost effort, then he will slay them, and see that they are denied the funeral rites due to brave warriors.
So when reading Pope’s translation we have to infer a hypothetical in “who flies”, by taking it to mean, “whoever flies (if anyone does)”. But we have to allow Pope some latitude, because of the constraints of his chosen form, the heroic couplet.