This got pretty long :)
Okay first of all the characters are all not dead. I keep seeing people say this but it's incorrect. Their souls were sucked out and being used as energy for Father. If anything I would say this is a fate worst then death but there is no reason why it cannot be reversed (and no you wouldn't need to break the rules of the FMA world to reverse it)
And yes I also don't think anyone who was turned into a philosopher stone was dead either. Hohenheim could still talk to all these souls. Ed heard the souls talking when they were in Envy as well. If they were dead this would not be possible. Their situation is different from the Amestrian Citizens because their bodies have long since decayed & disappeared. Thus sadly even if a way was discovered to bring them back they would have nothing to return too. That is not true for the citizens of Amestris whose bodies still exist.
In comparison Ed realized he could never bring his mother's soul back because she is dead. Whatever Ed created with human transmutation it would never be his mother. But the Amestrian souls are still there, just in Father.
And sure extracting the souls back has never been done before but I am assuming there is a way (reverse transmutation circle that Scar's Brother came up with) or Arakawa would not put everyone in this state. And no it's not cheap to bring them back because they are not dead to begin with. I am also hoping maybe the Xerxes souls (who can't return to their bodies) might be able to be released and die in peace.
The other thing in this chapter that I did not fully understand is Father said God is now a part of him. Now I do remember Ed reading the Xerxes ruins and interpreting as "bringing God down to Earth" but I am still a little confused about FMA's concept of God. I am guessing it's Truth and I have seen some people in the fandom say the God that Father pulled into himself is some universal truth. And actually that's an interesting concept (see I do praise fandom at times). I guess if everyone has an individual truth (which I believe is what the characters see when they open the doors) that there is also some universal truth that applies to everyone. And Father did say he opened Earth's door itself.
On another note Father was looking freaky in this chapter. Both as the black giant blob thing and as young Hohenheim's double. He's just an excellent baddie. Usually villains end up really annoying me (I am looking at you Naraku) but Father is just a villain I love to hate. XD