If someone says, "Hey, you. You go kill _______ or i'll kill you," you are not allowed to go kill that person. That's an extreme case. But in the case with Yitzchak, there was no 'Or i'll kill you.' So why did Avraham go to sacrifice Yitzchak? Was it because it was a direct commandment from Hashem? (Remember, Avraham also pleaded on behalf of the people of Sodom, who were Rasha'im. All the more so, he should plead on behalf of his son, who was also a Tzaddik!)
Yes this was very different because it was a direct command from Hashem. Don't forget, a Navi cannot ignore his nevuah.
The difference between this and Sedom was that from Avraham's perspective there was no reason for Hashem to warn him about the impending destruction except to get him to pray, so he did. By the Akeida he was commanded to carry out the action, so he did. Well, at least attempted to.
The merit of all ideals are measured in contrast to the will of Hashem. He now had clear direction as to what the will of Hashem.
While the severity of murder surpasses saving your own skin, it doesn't surpass Hashem's command. Beis Din is told to kill certain people, prophets told to kill certain people.
Sodom was a Gezeira, a heavenly judgment that he tried to weigh in on and add merit. This was a command from Hashem to him. It was not a judgement that you pray to have it changed as Moshe Rabbeinu did. It was saying to sacrifice his son.
Technically though, it was the wrong thing to do, since it was not actually Hashem's intention that he should kill Yitzchok. This also crossed Avraham Avinu's mind as we find the Medrash quoting different arguments the Satan have him to stop. After failing a few attempts the Satan told him it is just a test. To this, instead of refuting it, Avraham Avinu answered that the punishment of a liar is that you don't believe him even when he says the truth.
I once heard that Avraham Avinu couldn't actually do it. His hand stopped short, since all his limbs only did Hashem's will. This is alluded to in Nedarim, that Hashem gave him control over those limbs which we cannot control.