Paul might be asking Dr. Williams, "Do you not know that a little leaven leavens the whole lump of dough?"
I disagree. Williams is saying that not everything is "leaven" in this regard -- which is self evidently true; else every disagreement would be "leaven" of one sort or another, and there'd be as many churches as there are Christians.
However, he explicitly says that there are some things that "just do" qualify as "leaven" in the sense you've used the term, and he's pointed directly at ECUSA in that regard.
What he's really offering here is an invitation for ECUSA to formalize what it's been doing for years: leave. He won't say ECUSA is "wrong" (indeed, Williams actually agrees with ECUSA in many respects), but he recognizes that the ECUSA, as represented by its governing bodies, can no longer legitimately be regarded as part of the Anglican Communion.
The letter reminds me more of the scene in Acts 5:38-39, where Gamaliel warns the Pharisees, So in the present case I tell you, keep away from these men and let them alone, for if this plan or this undertaking is of man, it will fail; but if it is of God, you will not be able to overthrow them. You might even be found opposing God!" So they took his advice....
He's saying that the "non-Covenanters" are free to be in ecumenical relationship with the Anglican Communion, and that's really all it means. If they're "of God," they'll thrive. But if not, they'll wither away.