I think most episodes leave the viewer hanging on some things. That's why there are new episodes and new seasons and that's why the story moves forward and things are explained. If everything was so obvious and all the answers were there, there wouldn't be any reason to make a new episode or to keep watching the show.
The point of the first scene was actually to show how stressful Nacho's job is becoming and what sort of things he has to do. It shows the pressure is growing and the scene with the sewing machine shows just that. The stress, the pressure. I don't think it was disgusting. They didn't even show him beating the guy. Tuco's scene beating Mike was much more violent and they showed everything. The directors and creators of the show are innocent that you were having dinner while you were watching or that you were digusted, because it is completely subjective. That scene was surely not done with the purpose of causing disgust to the viewer.
but the rest of that scene was rather pointless
The fact that you (or anyone) don't understand the point of a scene, doesn't make it pointless. There are so many (apparently) pointless scene in Game of Thrones, for example, that the viewer will only understand the purpose of them seasons later.
Like I said, if the series was over right now, then yea, that scene with Lydia and other scenes would have been pointless, but I think you want answers too fast. If you don't understand something or if you are asking questions, isn't it a good sign? Isn't it better than the show and the story being too obvious?
why would he want to have innocent civilians (ie Nacho's father) operating for him?
I think it is pretty clear why, if you have been watching the show. Mike sabotaged his trucks, he lost people, Gus is doing better than him, he is in a desperate situation. Do you really think people in that kind of business give a shit about their employers' father, specially when they are in such a situation and when a lot of money is involved? He just wants a new way to get his drugs into the country and that's it.