Point of fact, Michael
does not say he has faith Harry will find another way to get rid of the Shadow. The exchange goes:
“I don’t know of another way to end Lasciel’s influence, but that
doesn’t mean there isn’t one out there. If you should change your
mind about the coin, Harry, if you want to get rid of it, I promise that
I’ll be there for you.”
So the closest he comes is a shrugging admission that there
might be another way and that he will help Harry if Harry decides to ditch the coin in the terms Michael has laid out.
Also, Michael isn't omniscient -- that's kind of the point Harry makes in Small Favor. Michael is working from biased, incomplete information.
He knows Harry grabbed the coin and got the Shadow.
The only way he knows of to get rid of the Shadow is for Harry to give up his magic.
Harry has not given up his magic. He has given the coin to Forthill, but Michael also knows the Denarians can summon their coins back and otherwise have found ways to get them back into circulation.
Also, Harry has been acting particularly odd lately (no blasting rod, not using fire).
Ergo, to the best of Michael's knowledge, Harry still has the Shadow, and the Shadow is most likely influencing him.