The end of Volume One

Firstly, Nathan had to fly him up high enough to get him away from the city just so Peter could explode without killing so many. He wasn't defused - the huge explosion was Peter exploding, not being defused. Secondly, I believe Nathan had the chance to fly off just before Peter exploded and so might have survived, but we'll have to see about that in the next season. Letting Claire shoot him in the head might have been a good option as they might have been able to remove the bullet later on so Peter could regenerate. Thing is, Claire was crying and incredibly upset and she didn't seem like she could actually shoot her own uncle. And as for Nathan's personal reasons for helping Peter, it's his brother. In his heart Nathan is a really good man so he probably felt like he needed to take a firm stand against his mother and at least save his daughter and the people of New York.

I think the idea was that shooting Peter in the head would kill him permanently. It would destroy his brain and wouldn't let him regenerate. Which doesn't explain why blowing up wouldn't also destroy his brain, but it's tv. Some things don't always make sense. So, just assuming that shooting Peter would somehow kill him for good, that was a big burden to put on a teenager. She'd be devastated to have to kill her uncle and friend. You could see how she was crying and sobbing. Nathan didn't want her to have to do that, or Peter to have to be responsible for killing everyone else. So he took the burden. And, the creator also said he just wanted Nathan to have a chance to be a hero, so maybe that's the whole answer;)