I've had some luck with this adaption: https://pastebin.com/d70TyxZq

const sql = await import("../libs/sql.js/sql-wasm.js");
window.initSqlJs = sql.initSqlJs;

using it together with geopackage.js like this:
...

initSqlJs({ locateFile: filename => "../libs/sql.js/sql-wasm.wasm" })
.then(async (SQL) => {
		const u8 = new Uint8Array(buffer);
		const data = await geopackage.open(u8);
		...

EDIT:
Okay, I'm not actually sure if this really works. It does seem to work but apparently geopackage.js bundles it's own sql.js. I still have to import sql.js or I will get an error. So I'm not sure if geopackage ends up using this ES module adaption, or it's own bundled sql.js.