It would do nothing to stop the Loup-Garou transformation. The spell lies dormant within Mcfin until the full moon rises, then it casts itself on him. The magical energy happens completely within his body, so the circle can't do anything about it (circles stop magic from crossing through them, they don't stop you from casting spells in them). Then, once he changed he'd be immune to magic and able to cross the circle with ease.
The circle did stop the Archive from using magic, that was the whole point, but shes a completely physical being, so nothing was stopping her from just leaving the circle and casting a spell.
It would have been useless to try to hide morgan in a magic circle, since Harry was well aware they would have come looking for him in Chicago anyway (plus the entire thing was a set up to keep them chasing Morgan).
A circle is like a wall. It doesn't stop you from casting spells in it. It just stops magic from crossing the perimeter.