I would say that my big question is this. When they installed the new perimeter drain and dug the trench, how did they not see this and offer you a solution? Wherever the water is coming from into this pit, it should have been incorporated into the water-guard system.
On a separate note...
It is very unlikely that jackhammering the basement slab will cause any damage in the walls on the main floor.
Here's why. It is very likely that your basement walls are resting on a footing. The floor slab is poured once the walls are in place. The floor slab in this case is not connected to...