It would take a little bit of refactoring of lil.js to avoid producing global references, and then you could wrap it all in a closure to expose a tidy public interface. Removing some parts of the Decker DOM and utility routines would help make such a distribution smaller (Though you definitely want to retain utility interfaces like RText, Bits, Array, and Image). You'd also want to polyfill certain builtins like show[] and print[] to allow them to be re-vectored into something useful for a given application or to remove them entirely, not unlike the repl.js stub used in the regression test suite.
I'm a bit hesitant to perform this surgery on Decker's main branch, because it would add some complexity and size to web-decker. If this is a project you're interested in pursuing I encourage it!