So I can assume still one thing, since they just been developing like any other civilisation without magical girls, they still manage to be able to create them? QB stated they didn't have emotions so....
I can also go with the lie theory because it is possible as well, hence that QB really don't give solid explanation about the whole universe relation with all this magic going on. It can help in progress as well it actually can hinder it as well, hence it is hard just like that say it is actually helping more than harming. Another funny thing is that they developed magic, not technology? So they can't just wish themselves? It gets a bit tricky, I can only assume that they actually have some limitations upon granting those wishes since there would probably be one or two of actually solving the universe problem... in the entire universe that is. That actually gives me the idea that the sole lie is based on having implement some sort of mind deceiving device that would actually project all the magic and such. Of course that would actually be a nice idea for a TV show as you probably already saw
Also the only wrong thing you do with being a god is to make progress for the people not make them have their own decisions. Progress is just a matter of time, and just maybe, if you would believe in it, Humanity would came up with more optimal and not harmful for anyone solution of the universe problem (If that is the case anyway, because why not just make that wish?....). Anyway what Madoka did isn't really what fixes "The problem", but it sure shows that the "progress" was not ruined by changing the rules, hence maybe it wouldn't change at all then?