And in this flea our two bloods mingled be. (line 4)
Although it sometimes seems that the speaker is all over the place, this poem actually proceeds in a very logical fashion. He sets up the idea of two bloodlines mixing, symbolizing marriage, within the first four lines.
O stay, three lives in one flea spare, Where we almost, yea, more than married are. (line 10-11)
The second stanza is directly focused on the idea of marriage. Using that single small word, "yea," as a bridge, the speaker makes the giant leap from "almost" to "more than." From this point on, he no longer even worries about trying to establish that a marriage has taken place; it's a given.
This flea is you and I, and this Our marriage bed, and marriage temple is. (line 12-13)
Maybe it's not the best idea to compare your marriage to a blood-sucking parasite...or to say that both the wedding and the honeymoon have taken place inside a bug.
Though parents grudge, and you, we're met, And cloister'd in these living walls of jet. (lines 14-15)
Nobody except the speaker is pleased that the marriage is going forward inside the church, or "cloister," of the flea's body, and it's as if he has tricked her into the wedding. That's the beauty of metaphors; they are sneaky little devils.
And sacrilege, three sins in killing three. (line 18)
Yes, sacrilege is a mortal sin, almost as bad as taking a life (your own or someone else's). In this case, the woman would be committing sacrilege against the holy institution of marriage, the joining of two souls in the eyes of God. But, hey there Donne, if you're so interested in souls, why do you seem so focused on the body, hmm?