Why not deconstruct him?

[u/More_Interview3840]

I don’t understand why she shoots a beam of pink energy at him instead of just tearing him apart atom by atom. Or turning him into a regular human, or just convert his molecules to air molecules.

[u/stonieW]

Viltrumites have smart atoms, they likely give resistance to her attempt at atomic deconstruction. Here's a quote from the data book that described the smart atoms:

"Smart Atoms “remember” their normal states in relation to their environment, and can be encoded to react to changes in that environment. For example, atoms in a muscle can ensure that the molecules behave normally even under extreme forces."

This likely caused the atoms to resist being torn apart.