The Builders die too easy thing isn't a big deal at all. Just the usual "technology looks like magic" sort of thing. They were in ships, flanked by incredible robots and shielded the whole time. The individual Builder was never portrayed like a god - their technology was.
I really like that this in NOW WAY changed Tony's origin, but just provided some interesting flavor to his family and introduced new characters. But there's not one single tiny change in the reality of how Tony grew up and became who he is now. I'm a huge fan of stories like this.
Based on what I've read so far, this has got to be some kind of "You guys broke space/time and so the higher powers have to step in to make things right. Here, this angel is going to police you dumb monkeys to make sure you do the right thing." Combined with everything happening in Avengers and New Avengers this could be some path toward introducing agents of the Living Tribunal into things to make the cosmic side of Marvel bigger.