In this cosmology, because these stones pre-exist the universe, they are dangerous even to those (like Odin and other godlike Asgaardians) who seem to have almost unlimited power.
There's supreme power. Then there is power beyond supreme power. Like Kierkegaard's teleological suspension of the ethical, aether represents the ontological suspension of the ontic (or something like that). It is being beyond being.
Certainly you can watch a movie like Thor and ignore the cosmological implications altogether. But with tantalizing mini-hints into worlds beyond worlds (like the short in the credits that introduces the collector, Taneleer Tivan), why would you? It's comic book joy and metaphysical frolicking all in one fabulous package.
So were there things that existed prior to creation?
This is actually a debate in early Christianity that, although to a certain degree resolved after the second century or so, still plays in some types of contemporary Christian theology. Here's a dramatically simplified outline.
In early Christianity, there was no dogmatic statement on whether creation came from nothing or something. The early Genesis accounts allow for multiple interpretations. One account seems to indicate creatio ex nihilo (creation out of nothing)... perhaps (see Genesis 2 and 1:1). The other account describes creation as being organized out of pre-existing elements (the earth was a formless void... the wind hovered over the waters, see Genesis 1:2-3). This is creatio ex materia.
* Side note, in the Marvel universe, there's actually a character named Ex Nihilo who can create new life on a planetary scale.
Over time, however, an orthodox consensus coalesced around the idea that God created ex nihilo. It has become the consensus tradition for most confessional Christian theologies, with a few notable exceptions, including individual theologians like Thomas Jay Oord, and movements such as process theology.
Depending on your perspective on things theological, you might consider the whole debate a kind of non-starter. However, there are some ways in which the debate has practical implications. Essentially, it boils down to a simple question.
Does God work with what exists or create that which God works with?
If the former, then God is primarily in the business of transforming and working with the given. God is always in a sense already "in" creation. For process theology, there is a sense in which God can never be considered or thought apart from creation, because God is always fully involved in temporal and material processes.
This former way of thinking can be a complicated rabbit hole to go down, but essentially it means there is no creation ex nihilo because God is always together relationally with creation, and never apart from it (a-material, eternal, unchanging, etc.).
If the latter, then God creates even the very things that God then desires or needs or hopes for. This way of thinking is illustrated nicely in the concluding thesis of Luther's Heidelberg Disputation, which reads, "The love of God does not find, but creates, that which is pleasing to it. The love of humans comes into being through that which is pleasing to them."
How we think about creation either out of nothing or out of pre-existing something (Infinity Stones, formless voids, etc.) then says at least a bit about how we are to approach the current creation we are a part of as it relates to either the nothing from which it emerged, or the pre-existing elements out of which it was formed.
What does all of this have to do with the Sovereignty of Christ?
Short version again. Most Christian traditions believe that Jesus was also the pre-existent LOGOS (Word). In other words, Jesus was both fully human, in creation, and also with God from the very beginning. Therefore Christ was not a creature of creation per se but a member of the Trinity that has always been (either creating everything out of nothing or forming things out of preceding stuff as the Word God speaks in/to/of creation).
Christ's sovereignty (we are coming up on Christ the King Sunday, after all) rests to a large degree on this dogmatic assertion, that Jesus the Son of Mary was also at the same time the incarnation of the pre-existent Logos. We can ignore at least for the time-being the liturgical insight that this is a relatively new feast in Christian tradition, the Feast of Our Lord Jesus Christ the King of the Universe, and therefore a rite in search of a theology.
Instead, focus on passages like Ephesian 1:21, which clearly set up Christ as ruler and authority over heaven and the universe as a whole. The Christ is what Loki wishes he could be, what Thor disavows, and what Odin is. Christ's sovereignty has to do, at least in part, with his power (whatever it means for Christ to have power) to bring about the kind of kingdom Christ has a mission to bring about.
So if the Christ rules, is there a sense in which Christ rules "beyond" sovereignty?
I always end up preaching on Christ the King Sunday some version of "Christ is a king, but not like any other king you know." Like Kierkegaard's suspension of the ethical, Christ seems to rule with an eschatological suspension of the sovereign. Christ does not seek or grasp sovereignty but is sovereign precisely through his sustaining and holding together his pre-existent divinity with his right now incarnation-ality.
Perhaps this is why we have such a hard time getting ahold of Jesus. We'd quite like him to be like us. But Jesus, like the aether and the Infinity Stones, comes at this mortal life both completely as a part of it, and completely apart from it at the same time. He is with us and in us precisely by being apart from us and outside of us. He is not us, and is just so one of us. He is the other in us, which is our own self.
That is Christ's sovereignty.
I could conclude with a quote from John Caputo in his The Insistence of God that I believe articulates the aether, Thor, and the sovereignty of Christ in a kind of phenomenological, radical theology register. Here you go:
"My theoretic (per)version of Hegel, my way of rereading Hegel, is to conceive a world in which the absolute would be neither substance nor subject but specter, in which 'substance' and 'subject' would only be provisional stand-in nomenclature we draw from the history of metaphysics for more nameless and boundless events, for events still unnamed, where Spirit has been weakened into the insistence of the event, into the specter of the peut-être" (145).
And for a great review of more graphic novels that engage the theological tradition, see Gregory Walter's post at The Christian Century, http://www.christiancentury.org/blogs/archive/2013-10/another-jesus-clone