1) the issue wasn't krypton, but what they had become. They were a society so constricted by what was good for the society rather than individual freedom. Having a natural child birth was jor-el's 'crime'. Freedom to live and choose includes the 'morons'. Jor-el warned the planet they were doomed, but the wouldn't listen.
2) yes, clark could have saved his dad, but the whole point of what Jonathan wanted was for his kid's powers to be hidden. Yes, it is irrational, but so are most parents.
3) they realize this, but for the most part cannot handle the new stimulus. That was the key issue. Superman had 30+ years to acclimate himself. The Kryptonians from the phantom zone had no such time.
They wanted to terraform earth, because that's what they did on all the other planets they explored. As with most people, the status quo is as far as they think