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?