As the topic suggests, I have a broken wall on the side of my building, I've "portaled out" all the windows, but what about the broken wall, can I just intersect the other brushes that make up the broken shape?

unfortunately...no

the only things that dont affect portalling are detail and model brushes

therefore when portalling your map - it is easier to hide the detail and model brushes - so that you dont even think about them

create a "false" wall out of your portal brush that is just inside the broken wall...this will seal off the cell you are creating

i would suggest taking a look at how wyatt added a "false" roof in his broken building in one of his portalling tutorial videos...i can't remeber which one it was though