And this, alas! is more than we would do. (line 9)
The speaker tries to make the woman feel guilty by expressing feelings of jealousy toward the flea. He conveniently forgets that insects and men play by different rules when it comes to women.
O stay, three lives in one flea spare, (line 10)
When the woman is about to crush the flea, the speaker appeals to her sense of power over it and, in a sense, over him. He's like, "You have the power to spare all of our lives." The subtext is, "If you kill all of us, you'll be a terrible, terrible person."
Though use make you apt to kill me, Let not to that self-murder added be, And sacrilege, three sins in killing three. (lines 16-18)
Now the speaker goes straight for the gut, with a guilt-trip that would make our Irish grandmother proud. He's like, "OK, maybe you think killing me wouldn't be such a big deal, but...you'd also be killing yourself and desecrating the sacrament of marriage." He brings religion into the mix, as these are all mortal sins in Christianity. The fate of the woman's everlasting soul depends on her not killing the flea!