Does it matter very much whether you betray either Pharae or the Matron Mother?
I saved the game before doing either, but when I swapped the fake eggs I ended up killing all the drow in the city but when I went to leave it said the Matron sealed the city. When I went looking for the wench she is nowhere to be found?

Did you already wax Solaufein? If not, he should have appeared and given you some insight into this choice. If you did kill him earlier, you're probably better off just following along with Phaere's plan. If you betray her to the Matron, you're going to have a titantic battle on your hands, one that is undoubtedly going to require a few reloaded saves...