User blog comment:EmpyreanSmoke/Supernatural Q&A/@comment-3045936-20150729055227/@comment-24834479-20150805214123

1. Iron can effect the magical powers of ghosts, demons, fairies, some monsters, and possibly some gods. It does not conceal the magic of all users, as beings such as angels are unaffected. Iron only prohibits the affected being from using his or her magical powers. They are still able to use magic should the source be anything but them. This is why Crowley was able to use the blood call, and why Rowena was able to remove the Mark of Cain.

2. The origin of the Levitahn might be explained more as we learn about the Darkness. The lore from Supernatural is based off the Bible, but we do not keep everything the same. Michael slaying a leviathan on Earth is not within the Supernatural universe.

3. When Castiel became God from absorbing all of those souls, he became powerful enough to kill archangels. He didn't want them out of their cage because he didn't want to deal with another threat.