It all depends upon the tools at hand. If the workpiece were on the order of 2" square, it would take an extra long end mill to side mill the end. Even if the machinist had an end mill with 2" flutes, it would be prone to chatter. Facing may be the only option available.
I would cut all four long faces first. I would take pains to square up the stock. The fixed jaw of the vise would need to be vertical. The direction of cut would be along y, with shallow depth of cut. A small width of cut will keep most of the cutting force in the y direction and minimize having the workpiece pull free.
If there is concern about the ability to square in the x direction, once the facing operation was complete, the workpiece could be rotated 90º which will place a squared edge on the floor of the vise. Repeat the facing process and you would have a squared end. Flip the workpiece over and face the opposite end to dimension.