These lines need to be interpreted in the context of the complete stanza:
Thus I entered, and thus I go!
In triumphs, people have dropped down dead.
"Paid by the world, what dost thou owe
Me?"—God might question; now instead,
'Tis God shall repay: I am safer so.
There is an enjambment between the third and fourth lines of the stanza: that is, the clause runs over from one line to the next. You need to read it like this:
“Paid by the world, what dost thou owe me?”—God might question [them thus]
So this is not a question that the speaker is asking God, but rather a question that the speaker imagines that God might ask of the “people who have dropped down dead in triumphs” from the second line. These (hypothetical) people have died at the height of their successes, “paid by the world” with banners, bells, and cheering, as in the first two stanzas of the poem; and earthly rewards, as in the third stanza. God, the speaker implies, would judge these people for their sins of pride and avarice. The enjambment strikingly places the word “me” (that is, God) at the start of the next line, emphasizing the awfulness of God’s judgement.
However, the speaker did not “drop down dead in triumphs”, but survived to be repaid in ironic fashion, humiliated and dragged to the scaffold to be publicly executed. The speaker has repented of their sins, and so they will be rewarded in heaven: that’s the meaning of “’Tis God shall repay [me]” in the last line. A martyr’s death, the speaker says, is “safer” than a hero’s death, because it guarantees Christian salvation.