Premise: Humans are essentially embodied.There are at least two theological counterexamples. One is that humans survive death until the resurrection. The other is that Jesus descended into hell while his body was still in the tomb. If either are true then humans are not essentially embodied (provided that one is a human essentially).
To that, M.C. responded that there is no good Biblical evidence that Jesus went to hell, citing 1 Peter 3:19, Revelation 20:3, and that in the Creed it refers to Hades where dead bodies go.
Here, I do not wish to argue for any definitive theological proposition, rather I will point out potential options available to make sense of the empty tomb. This is a rough sketch. I will avoid arguments in favor of and problems with each view, though for a couple I point out some difficulties.
In becoming human, the Son took on a human nature.
1. In taking on a human nature, the Son took on a human body and soul. Jesus was part body and part soul (hylomorphism). He died and his body was placed in a tomb. Jesus was not the dead body. Instead, he continued to exist (in Hades/Hell, wherever) immaterially (though as a human and not merely God-immaterially.) Instead of having a body as a proper part, he had only a soul.
2. Same as 1 only upon dying, Jesus becomes his soul.
But this seems extremely implausible. For surely if I am not identical with a proper part of myself now, then I could not become that thing for which I was not identical.
3. The Son takes on a human soul (e.g., Cartesian dualism). He died and his body was placed in a tomb. Jesus was not the dead body. In fact, he was never a body and never had a body as a proper part. (He had a body in the sense that he was intimately causally related to it, but he was not constituted by the body.) Instead, he continued to exist (in Hades/hell, wherever) as immaterial as he always had since the Incarnation.
4. Jesus becomes a human body (or brain or part of a brain). He dies. Now what? He either becomes a dead body or not. If he becomes a dead body, then Jesus is not essentially living, which seems theologically implausible (he would at least temporarily be conquered by death). Furthermore, a dead body seems to be nothing more than a collection of material parts--there is not one thing over and above the collection of parts organized and unified such that there is one more thing in addition to the parts--a corpse. So one thing becomes many things, a contradiction.
Did Christ go out of existence? Then one member of the Trinity ceases to exist which seems theologically problematic.
Did he continue to exist by becoming part of his body? Then the same problem rears its head as in 2 above.
Did his body "shrink" to say, part of his brain, and he continued to exist in Hades or Sheol while the corpse was in the tomb? And does this happen to all of us? Then the significance of death loses force since death is like losing a limb (or several limbs).
Perhaps Jesus then becomes a human soul, surviving until his resurrection. But then we lose some motivation for the thesis that he becomes a human body.
5. The same as 4 except that when Jesus dies he becomes a different body while his first body was in the tomb. But then where does he go? Hades (Sheol, wherever)--where the dead bodies are supposed to go? But his first body is still in the tomb. Why does it remain in the tomb? Perhaps one might offer that he becomes some sort of ephemeral ghost-like body, which takes up space but isn't solid like Casper. But is there is any independent motivation for such a view?